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1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.43119676,log10 basal metabolic rate (kcal): 1639,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.83148599,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.876907474,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.15,fat mass (%): 15.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.488844346,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 34.5,log10 homair (insulin resistance index based on homa): -0.052239618,log10 homais (insulin secretion index based on homa): 1.502675359,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.432375938,insgenin (insulinogenic index): 2.21988053,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.389927647,log10 matsuda insulin sensitivity index: 1.00329206,muscle mass (%): 48.3,lg10 serum c-reactive protein (mg/l): -0.375717904,lg10 plasma adiponectin (mg/l): 0.748188027,ogtt fasting plasma free fatty acid (mmol/l): 0.27,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 8,ogtt 120 min plasma glucose (mmol/l): 3.4,log10 il1 receptor antagonist (pg/ml): 2.133123575,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.544068044,ogtt 30 min plasma insulin (mu/l): 1.82672252,ogtt 120 min plasma insulin (mu/l): 0.982271233,log10 ogtt fasting plasma proinsulin (pm/l): 0.954242509,ogtt 30 min plasma proinsulin (pm/l): 1.257678575,ogtt 120 min plasma proinsulin (pm/l): 1.225309282,log10 bioimpedance: Resistance: 2.571708832,log10 bioimpedance (reactance): 1.579783597,waist to hip ratio: 0.979166667,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.079181246,log10 creatinine (umol/l): 1.819543936,log10 total cholesterol (mmol/l): 0.71432976,log10 ldl cholesterol (mmol/l): 0.498310554,log10 hdl cholesterol (mmol/l): 0.10720997,log10 total triglycerides (mmol/l): -0.022276395,log10 serum apoa1 (g/l): 0.149219113,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 0.995972511 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098268 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249167,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978095 | GSM1098268 | GSE45159 | 0.334419 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2044 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249167 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978095 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.460539045,log10 basal metabolic rate (kcal): 1480,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.977929407,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.106357611,plasma free fatty acids under the curve ogtt (mmol/l * min): 32.25,fat mass (%): 23.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.11048331,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 301.5,log10 homair (insulin resistance index based on homa): 0.629228322,log10 homais (insulin secretion index based on homa): 1.951216055,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.919679409,insgenin (insulinogenic index): 1.997823081,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.862244711,log10 matsuda insulin sensitivity index: 0.293811986,muscle mass (%): 42.7,lg10 serum c-reactive protein (mg/l): 0.2509077,lg10 plasma adiponectin (mg/l): 0.86923172,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.39,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 6.7,ogtt 30 min plasma glucose (mmol/l): 10.3,ogtt 120 min plasma glucose (mmol/l): 8.6,log10 il1 receptor antagonist (pg/ml): 2.208924831,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.155336037,ogtt 30 min plasma insulin (mu/l): 1.86923172,ogtt 120 min plasma insulin (mu/l): 2.310480891,log10 ogtt fasting plasma proinsulin (pm/l): 1.643452676,ogtt 30 min plasma proinsulin (pm/l): 1.900913068,ogtt 120 min plasma proinsulin (pm/l): 2.301247089,log10 bioimpedance: Resistance: 2.705007959,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 1.068627451,log10 serum bilirubin (umol/l): 1.380211242,log10 serum alanine aminotransfrase (u/l): 1.447158031,log10 creatinine (umol/l): 1.785329835,log10 total cholesterol (mmol/l): 0.747411808,log10 ldl cholesterol (mmol/l): 0.519827994,log10 hdl cholesterol (mmol/l): 0.257678575,log10 total triglycerides (mmol/l): -0.004364805,log10 serum apoa1 (g/l): 0.238046103,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 0.984466492 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098269 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249168,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978096 | GSM1098269 | GSE45159 | 0.288496 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2057 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249168 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978096 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.400414628,log10 basal metabolic rate (kcal): 1541,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.330401821,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.463300239,plasma free fatty acids under the curve ogtt (mmol/l * min): 9.9,fat mass (%): 15.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.587777516,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 121.5,log10 homair (insulin resistance index based on homa): -0.188424994,log10 homais (insulin secretion index based on homa): 1.453640159,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.092545208,insgenin (insulinogenic index): 1.80106053,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.018325945,log10 matsuda insulin sensitivity index: 1.219531313,muscle mass (%): 45.6,lg10 serum c-reactive protein (mg/l): 1.210612766,lg10 plasma adiponectin (mg/l): 0.770852012,ogtt fasting plasma free fatty acid (mmol/l): 0.2,ogtt 30 min plasma free fatty acid (mmol/l): 0.1,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 7.8,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.38790569,log10 il1 beta (pg/ml): -0.638272164,log10 ogtt fasting plasma insulin (mu/l): 0.431363764,ogtt 30 min plasma insulin (mu/l): 1.447158031,ogtt 120 min plasma insulin (mu/l): 0.880813592,log10 ogtt fasting plasma proinsulin (pm/l): 0.763427994,ogtt 30 min plasma proinsulin (pm/l): 1.190331698,ogtt 120 min plasma proinsulin (pm/l): 1.23299611,log10 bioimpedance: Resistance: 2.615950052,log10 bioimpedance (reactance): 1.531478917,waist to hip ratio: 0.907216495,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.954242509,log10 total cholesterol (mmol/l): 0.695481676,log10 ldl cholesterol (mmol/l): 0.53529412,log10 hdl cholesterol (mmol/l): 0.012837225,log10 total triglycerides (mmol/l): 0.068185862,log10 serum apoa1 (g/l): 0.056904851,log10 serum apob (g/l): 0.008600172,log10 urinary albumin excretion rate (ug/min): 0.524173216 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098270 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249169,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978097 | GSM1098270 | GSE45159 | 0.120527 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2100 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249169 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978097 |
|
1 | age: 48,tissue: adipose tissue,log10 body mass index: 1.46075309,log10 basal metabolic rate (kcal): 1604,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.701436771,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.102011059,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.95,fat mass (%): 23.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.243173983,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 6,log10 homair (insulin resistance index based on homa): 0.296177493,log10 homais (insulin secretion index based on homa): 2.074328743,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.804337104,insgenin (insulinogenic index): 2.859830842,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.758313758,log10 matsuda insulin sensitivity index: 0.678437918,muscle mass (%): 42.7,lg10 serum c-reactive protein (mg/l): 0.514946005,lg10 plasma adiponectin (mg/l): 0.643452676,ogtt fasting plasma free fatty acid (mmol/l): 0.24,ogtt 30 min plasma free fatty acid (mmol/l): 0.1,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5,ogtt 30 min plasma glucose (mmol/l): 6.3,ogtt 120 min plasma glucose (mmol/l): 3.4,log10 il1 receptor antagonist (pg/ml): 2.308841761,log10 il1 beta (pg/ml): -0.795880017,log10 ogtt fasting plasma insulin (mu/l): 0.949390007,ogtt 30 min plasma insulin (mu/l): 2.219584526,ogtt 120 min plasma insulin (mu/l): 1.079181246,log10 ogtt fasting plasma proinsulin (pm/l): 1.086359831,ogtt 30 min plasma proinsulin (pm/l): 1.828015064,ogtt 120 min plasma proinsulin (pm/l): 1.729974286,log10 bioimpedance: Resistance: 2.670245853,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 1.019607843,log10 serum bilirubin (umol/l): 0.954242509,log10 serum alanine aminotransfrase (u/l): 1.72427587,log10 creatinine (umol/l): 1.86923172,log10 total cholesterol (mmol/l): 0.715167358,log10 ldl cholesterol (mmol/l): 0.507855872,log10 hdl cholesterol (mmol/l): 0.176091259,log10 total triglycerides (mmol/l): 0.056904851,log10 serum apoa1 (g/l): 0.184691431,log10 serum apob (g/l): -0.008773924,log10 urinary albumin excretion rate (ug/min): 1.004021274 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098271 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249170,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978098 | GSM1098271 | GSE45159 | 0.271736 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2126 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249170 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978098 |
|
1 | age: 48,tissue: adipose tissue,log10 body mass index: 1.416382864,log10 basal metabolic rate (kcal): 1483,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.635274288,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.771993308,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.9,fat mass (%): 18,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.329796338,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 19.5,log10 homair (insulin resistance index based on homa): 0.035918683,log10 homais (insulin secretion index based on homa): 1.742678932,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.077113432,insgenin (insulinogenic index): 2.109144469,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.932423026,log10 matsuda insulin sensitivity index: 1.123139524,muscle mass (%): 45.2,lg10 serum c-reactive protein (mg/l): -0.278189385,lg10 plasma adiponectin (mg/l): 1.012837225,ogtt fasting plasma free fatty acid (mmol/l): 0.33,ogtt 30 min plasma free fatty acid (mmol/l): 0.16,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 5.9,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.198849453,log10 il1 beta (pg/ml): -0.585026652,log10 ogtt fasting plasma insulin (mu/l): 0.672097858,ogtt 30 min plasma insulin (mu/l): 1.294466226,ogtt 120 min plasma insulin (mu/l): 1.214843848,log10 ogtt fasting plasma proinsulin (pm/l): 0.908485019,ogtt 30 min plasma proinsulin (pm/l): 1.012837225,ogtt 120 min plasma proinsulin (pm/l): 1.257678575,log10 bioimpedance: Resistance: 2.658011397,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 0.962566845,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.301029996,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.720985744,log10 ldl cholesterol (mmol/l): 0.553883027,log10 hdl cholesterol (mmol/l): 0.113943352,log10 total triglycerides (mmol/l): -0.187086643,log10 serum apoa1 (g/l): 0.113943352,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 0.529443953 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098272 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249171,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978099 | GSM1098272 | GSE45159 | 0.126368 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2165 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249171 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978099 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.289744126,log10 basal metabolic rate (kcal): 1382,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.781997935,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.439979165,plasma free fatty acids under the curve ogtt (mmol/l * min): 14.4,fat mass (%): 11,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.05663772,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 513,log10 homair (insulin resistance index based on homa): -0.036212173,log10 homais (insulin secretion index based on homa): 1.912849824,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.136942413,insgenin (insulinogenic index): 1.268384278,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.019822224,log10 matsuda insulin sensitivity index: 1.071467197,muscle mass (%): 49.9,lg10 serum c-reactive protein (mg/l): 0.02201574,lg10 plasma adiponectin (mg/l): 1.281033367,ogtt fasting plasma free fatty acid (mmol/l): 0.58,ogtt 30 min plasma free fatty acid (mmol/l): 0.08,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 4.6,ogtt 30 min plasma glucose (mmol/l): 13.3,ogtt 120 min plasma glucose (mmol/l): 4.4,log10 il1 receptor antagonist (pg/ml): 2.167966813,log10 il1 beta (pg/ml): -0.537602002,log10 ogtt fasting plasma insulin (mu/l): 0.653212514,ogtt 30 min plasma insulin (mu/l): 1.496929648,ogtt 120 min plasma insulin (mu/l): 0.86923172,log10 ogtt fasting plasma proinsulin (pm/l): 0.826074803,ogtt 30 min plasma proinsulin (pm/l): 1.376576957,ogtt 120 min plasma proinsulin (pm/l): 1.505149978,log10 bioimpedance: Resistance: 2.761927838,log10 bioimpedance (reactance): 1.77815125,waist to hip ratio: 0.934065934,log10 serum bilirubin (umol/l): 0.954242509,log10 serum alanine aminotransfrase (u/l): 1.204119983,log10 creatinine (umol/l): 1.84509804,log10 total cholesterol (mmol/l): 0.678518379,log10 ldl cholesterol (mmol/l): 0.338456494,log10 hdl cholesterol (mmol/l): 0.389166084,log10 total triglycerides (mmol/l): -0.244125144,log10 serum apoa1 (g/l): 0.271841607,log10 serum apob (g/l): -0.22184875,log10 urinary albumin excretion rate (ug/min): 0.633822004 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098273 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249172,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978100 | GSM1098273 | GSE45159 | 0.302944 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2176 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249172 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978100 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.448257751,log10 basal metabolic rate (kcal): 1499,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.945923049,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.179080503,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.3,fat mass (%): 23.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.955649908,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 369,log10 homair (insulin resistance index based on homa): 0.045062063,log10 homais (insulin secretion index based on homa): 1.751822312,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.321411998,insgenin (insulinogenic index): 1.515211304,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.243162115,log10 matsuda insulin sensitivity index: 0.925955413,muscle mass (%): 41.8,lg10 serum c-reactive protein (mg/l): -0.064492734,lg10 plasma adiponectin (mg/l): 0.897627091,ogtt fasting plasma free fatty acid (mmol/l): 0.24,ogtt 30 min plasma free fatty acid (mmol/l): 0.23,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 10,ogtt 120 min plasma glucose (mmol/l): 7,log10 il1 receptor antagonist (pg/ml): 2.328990855,log10 il1 beta (pg/ml): -0.958607315,log10 ogtt fasting plasma insulin (mu/l): 0.681241237,ogtt 30 min plasma insulin (mu/l): 1.491361694,ogtt 120 min plasma insulin (mu/l): 1.540329475,log10 ogtt fasting plasma proinsulin (pm/l): 1.217483944,ogtt 30 min plasma proinsulin (pm/l): 1.567026366,ogtt 120 min plasma proinsulin (pm/l): 1.844477176,log10 bioimpedance: Resistance: 2.715167358,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.980392157,log10 serum bilirubin (umol/l): 0.954242509,log10 serum alanine aminotransfrase (u/l): 1.361727836,log10 creatinine (umol/l): 1.799340549,log10 total cholesterol (mmol/l): 0.749736316,log10 ldl cholesterol (mmol/l): 0.58546073,log10 hdl cholesterol (mmol/l): 0.100370545,log10 total triglycerides (mmol/l): 0.28780173,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): 0.10720997,log10 urinary albumin excretion rate (ug/min): 0.486076097 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098274 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249173,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978101 | GSM1098274 | GSE45159 | 0.196345 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2261 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249173 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978101 |
|
1 | age: 48,tissue: adipose tissue,log10 body mass index: 1.431687673,log10 basal metabolic rate (kcal): 1817,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.592582972,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.093259407,plasma free fatty acids under the curve ogtt (mmol/l * min): 14.55,fat mass (%): 23.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.764871591,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 174,log10 homair (insulin resistance index based on homa): 0.471943316,log10 homais (insulin secretion index based on homa): 2,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.615865919,insgenin (insulinogenic index): 2.180535471,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.518671836,log10 matsuda insulin sensitivity index: 0.605773602,muscle mass (%): 44.4,lg10 serum c-reactive protein (mg/l): -0.387216143,lg10 plasma adiponectin (mg/l): 0.73239376,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 5,log10 il1 receptor antagonist (pg/ml): 2.382539323,log10 il1 beta (pg/ml): -0.886056648,log10 ogtt fasting plasma insulin (mu/l): 1.06069784,ogtt 30 min plasma insulin (mu/l): 1.999565488,ogtt 120 min plasma insulin (mu/l): 1.201397124,log10 ogtt fasting plasma proinsulin (pm/l): 1.136720567,ogtt 30 min plasma proinsulin (pm/l): 1.618048097,ogtt 120 min plasma proinsulin (pm/l): 1.501059262,log10 bioimpedance: Resistance: 2.701567985,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 0.927927928,log10 serum bilirubin (umol/l): 1.255272505,log10 serum alanine aminotransfrase (u/l): 1.806179974,log10 creatinine (umol/l): 1.897627091,log10 total cholesterol (mmol/l): 0.758154622,log10 ldl cholesterol (mmol/l): 0.607455023,log10 hdl cholesterol (mmol/l): 0.075546961,log10 total triglycerides (mmol/l): 0.149219113,log10 serum apoa1 (g/l): 0.117271296,log10 serum apob (g/l): 0.093421685,log10 urinary albumin excretion rate (ug/min): -0.114284109 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098275 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249174,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978102 | GSM1098275 | GSE45159 | 0.258599 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2338 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249174 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978102 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.418238088,log10 basal metabolic rate (kcal): 1597,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.617519331,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.880035694,plasma free fatty acids under the curve ogtt (mmol/l * min): 14.4,fat mass (%): 24.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.553629294,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 67.5,log10 homair (insulin resistance index based on homa): -0.064828745,log10 homais (insulin secretion index based on homa): 1.490086232,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.511027292,insgenin (insulinogenic index): 2.207125493,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.476947502,log10 matsuda insulin sensitivity index: 0.960575615,muscle mass (%): 43.6,lg10 serum c-reactive protein (mg/l): -0.170053304,lg10 plasma adiponectin (mg/l): 0.826074803,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.13,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 8.4,ogtt 120 min plasma glucose (mmol/l): 3.6,log10 il1 receptor antagonist (pg/ml): 2.606875578,log10 il1 beta (pg/ml): -0.431798276,log10 ogtt fasting plasma insulin (mu/l): 0.531478917,ogtt 30 min plasma insulin (mu/l): 1.880241776,ogtt 120 min plasma insulin (mu/l): 1.250420002,log10 ogtt fasting plasma proinsulin (pm/l): 0.973127854,ogtt 30 min plasma proinsulin (pm/l): 1.460897843,ogtt 120 min plasma proinsulin (pm/l): 1.580924976,log10 bioimpedance: Resistance: 2.773054693,log10 bioimpedance (reactance): 1.857332496,waist to hip ratio: 0.903846154,log10 serum bilirubin (umol/l): 1.431363764,log10 serum alanine aminotransfrase (u/l): 1.505149978,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.715167358,log10 ldl cholesterol (mmol/l): 0.522444234,log10 hdl cholesterol (mmol/l): 0.158362492,log10 total triglycerides (mmol/l): -0.036212173,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): 0.017033339,log10 urinary albumin excretion rate (ug/min): 0.618048097 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098276 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249175,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978103 | GSM1098276 | GSE45159 | 0.131633 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2392 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249175 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978103 |
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1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.383155622,log10 basal metabolic rate (kcal): 1695,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.518575523,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.639803829,plasma free fatty acids under the curve ogtt (mmol/l * min): 24.6,fat mass (%): 17,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.706496018,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 199.5,log10 homair (insulin resistance index based on homa): 0.034851183,log10 homais (insulin secretion index based on homa): 1.708515322,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.329540248,insgenin (insulinogenic index): 1.817961805,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.256356886,log10 matsuda insulin sensitivity index: 0.956161572,muscle mass (%): 49.8,lg10 serum c-reactive protein (mg/l): -0.54668166,lg10 plasma adiponectin (mg/l): 0.934498451,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.31,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.3,ogtt 30 min plasma glucose (mmol/l): 7.8,ogtt 120 min plasma glucose (mmol/l): 6.4,log10 il1 receptor antagonist (pg/ml): 2.228349021,log10 il1 beta (pg/ml): -0.795880017,log10 ogtt fasting plasma insulin (mu/l): 0.662757832,ogtt 30 min plasma insulin (mu/l): 1.505149978,ogtt 120 min plasma insulin (mu/l): 1.542825427,log10 ogtt fasting plasma proinsulin (pm/l): 0.86923172,ogtt 30 min plasma proinsulin (pm/l): 1.021189299,ogtt 120 min plasma proinsulin (pm/l): 1.5289167,log10 bioimpedance: Resistance: 2.683047038,log10 bioimpedance (reactance): 1.785329835,waist to hip ratio: 0.967741935,log10 serum bilirubin (umol/l): 1.204119983,log10 serum alanine aminotransfrase (u/l): 1.301029996,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.762678564,log10 ldl cholesterol (mmol/l): 0.580924976,log10 hdl cholesterol (mmol/l): 0.195899652,log10 total triglycerides (mmol/l): 0.161368002,log10 serum apoa1 (g/l): 0.184691431,log10 serum apob (g/l): 0.079181246,log10 urinary albumin excretion rate (ug/min): 0.898617296 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098277 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249176,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978104 | GSM1098277 | GSE45159 | 0.220364 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2415 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249176 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978104 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.445909431,log10 basal metabolic rate (kcal): 1683,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.601836376,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.049394709,plasma free fatty acids under the curve ogtt (mmol/l * min): 21.6,fat mass (%): 24.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.897845456,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 210,log10 homair (insulin resistance index based on homa): 0.493287615,log10 homais (insulin secretion index based on homa): 1.922744675,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.613112102,insgenin (insulinogenic index): 1.738384124,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.517129891,log10 matsuda insulin sensitivity index: 0.543760768,muscle mass (%): 42.7,lg10 serum c-reactive protein (mg/l): -0.120330794,lg10 plasma adiponectin (mg/l): 0.716003344,ogtt fasting plasma free fatty acid (mmol/l): 0.35,ogtt 30 min plasma free fatty acid (mmol/l): 0.25,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.2,ogtt 30 min plasma glucose (mmol/l): 9.4,ogtt 120 min plasma glucose (mmol/l): 6.6,log10 il1 receptor antagonist (pg/ml): 2.173069664,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.053078443,ogtt 30 min plasma insulin (mu/l): 1.607455023,ogtt 120 min plasma insulin (mu/l): 1.974050903,log10 ogtt fasting plasma proinsulin (pm/l): 1.017033339,ogtt 30 min plasma proinsulin (pm/l): 1.227886705,ogtt 120 min plasma proinsulin (pm/l): 1.586587305,log10 bioimpedance: Resistance: 2.7084209,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.990654206,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.51851394,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.745074792,log10 ldl cholesterol (mmol/l): 0.550228353,log10 hdl cholesterol (mmol/l): 0.152288344,log10 total triglycerides (mmol/l): 0.079181246,log10 serum apoa1 (g/l): 0.173186268,log10 serum apob (g/l): 0.045322979,log10 urinary albumin excretion rate (ug/min): 0.579783597 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098278 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249177,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978105 | GSM1098278 | GSE45159 | 0.27323 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2426 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249177 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978105 |
|
1 | age: 46,tissue: adipose tissue,log10 body mass index: 1.430377851,log10 basal metabolic rate (kcal): 1675,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.830373043,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.108435981,plasma free fatty acids under the curve ogtt (mmol/l * min): 12,fat mass (%): 21.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.607330314,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 84,log10 homair (insulin resistance index based on homa): 0.19657531,log10 homais (insulin secretion index based on homa): 1.724631995,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.470645658,insgenin (insulinogenic index): 2.0805363,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.400779677,log10 matsuda insulin sensitivity index: 0.840071746,muscle mass (%): 46.2,lg10 serum c-reactive protein (mg/l): 0.348304863,lg10 plasma adiponectin (mg/l): 0.982271233,ogtt fasting plasma free fatty acid (mmol/l): 0.23,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 3.4,log10 il1 receptor antagonist (pg/ml): 2.120211868,log10 il1 beta (pg/ml): -0.795880017,log10 ogtt fasting plasma insulin (mu/l): 0.785329835,ogtt 30 min plasma insulin (mu/l): 1.846955325,ogtt 120 min plasma insulin (mu/l): 1.136720567,log10 ogtt fasting plasma proinsulin (pm/l): 1.025305865,ogtt 30 min plasma proinsulin (pm/l): 1.330413773,ogtt 120 min plasma proinsulin (pm/l): 1.348304863,log10 bioimpedance: Resistance: 2.693726949,log10 bioimpedance (reactance): 1.792391689,waist to hip ratio: 0.994897959,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.51851394,log10 creatinine (umol/l): 1.838849091,log10 total cholesterol (mmol/l): 0.825426118,log10 ldl cholesterol (mmol/l): 0.57054294,log10 hdl cholesterol (mmol/l): 0.274157849,log10 total triglycerides (mmol/l): 0.281033367,log10 serum apoa1 (g/l): 0.294466226,log10 serum apob (g/l): 0.130333768,log10 urinary albumin excretion rate (ug/min): 0.62324929 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098279 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249178,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978106 | GSM1098279 | GSE45159 | 0.287158 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2474 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249178 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978106 |
|
1 | age: 46,tissue: adipose tissue,log10 body mass index: 1.436515655,log10 basal metabolic rate (kcal): 1738,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.246235106,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.743723019,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.05,fat mass (%): 23.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.46454575,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 82.5,log10 homair (insulin resistance index based on homa): 0.35945602,log10 homais (insulin secretion index based on homa): 2.066216269,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.554016449,insgenin (insulinogenic index): 2.177948544,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.457624573,log10 matsuda insulin sensitivity index: 0.731711247,muscle mass (%): 44.4,lg10 serum c-reactive protein (mg/l): -0.140261434,lg10 plasma adiponectin (mg/l): 0.643452676,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 8,ogtt 120 min plasma glucose (mmol/l): 3.3,log10 il1 receptor antagonist (pg/ml): 2.406812593,log10 il1 beta (pg/ml): -0.236572006,log10 ogtt fasting plasma insulin (mu/l): 0.995635195,ogtt 30 min plasma insulin (mu/l): 1.904174368,ogtt 120 min plasma insulin (mu/l): 1.350248018,log10 ogtt fasting plasma proinsulin (pm/l): 1.093421685,ogtt 30 min plasma proinsulin (pm/l): 1.51851394,ogtt 120 min plasma proinsulin (pm/l): 1.661812686,log10 bioimpedance: Resistance: 2.705007959,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 0.962962963,log10 serum bilirubin (umol/l): 0.84509804,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.991226076,log10 total cholesterol (mmol/l): 0.797959644,log10 ldl cholesterol (mmol/l): 0.62324929,log10 hdl cholesterol (mmol/l): 0.012837225,log10 total triglycerides (mmol/l): 0.301029996,log10 serum apoa1 (g/l): 0.123851641,log10 serum apob (g/l): 0.155336037,log10 urinary albumin excretion rate (ug/min): 0.857872328 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098280 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249179,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978107 | GSM1098280 | GSE45159 | 0.227872 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2488 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249179 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978107 |
|
1 | age: 53,tissue: adipose tissue,log10 body mass index: 1.409302874,log10 basal metabolic rate (kcal): 1697,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.58477133,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.62351565,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.35,fat mass (%): 18.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.754887502,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 192,log10 homair (insulin resistance index based on homa): 0.068103367,log10 homais (insulin secretion index based on homa): 1.650908559,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.419476604,insgenin (insulinogenic index): 1.827369273,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.35958887,log10 matsuda insulin sensitivity index: 0.895535625,muscle mass (%): 51.5,lg10 serum c-reactive protein (mg/l): 0.057285644,lg10 plasma adiponectin (mg/l): 0.886490725,ogtt fasting plasma free fatty acid (mmol/l): 0.36,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 5.2,log10 il1 receptor antagonist (pg/ml): 2.034146977,log10 il1 beta (pg/ml): -0.537602002,log10 ogtt fasting plasma insulin (mu/l): 0.672097858,ogtt 30 min plasma insulin (mu/l): 1.64246452,ogtt 120 min plasma insulin (mu/l): 1.57054294,log10 ogtt fasting plasma proinsulin (pm/l): 0.973127854,ogtt 30 min plasma proinsulin (pm/l): 1.190331698,ogtt 120 min plasma proinsulin (pm/l): 1.610660163,log10 bioimpedance: Resistance: 2.679427897,log10 bioimpedance (reactance): 1.875061263,waist to hip ratio: 0.904040404,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.041392685,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.730782276,log10 ldl cholesterol (mmol/l): 0.552668216,log10 hdl cholesterol (mmol/l): 0.161368002,log10 total triglycerides (mmol/l): -0.142667504,log10 serum apoa1 (g/l): 0.133538908,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 1.021189299 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098281 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249180,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978108 | GSM1098281 | GSE45159 | 0.209118 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2495 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249180 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978108 |
|
1 | age: 48,tissue: adipose tissue,log10 body mass index: 1.406526027,log10 basal metabolic rate (kcal): 1668,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.86687903,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.14583956,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.25,fat mass (%): 20.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.918117851,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 271.5,log10 homair (insulin resistance index based on homa): 0.554260276,log10 homais (insulin secretion index based on homa): 2.08231696,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.727955835,insgenin (insulinogenic index): 2.118733698,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.637919808,log10 matsuda insulin sensitivity index: 0.480664132,muscle mass (%): 45.1,lg10 serum c-reactive protein (mg/l): -0.539102157,lg10 plasma adiponectin (mg/l): 0.707570176,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 10.1,ogtt 120 min plasma glucose (mmol/l): 6.1,log10 il1 receptor antagonist (pg/ml): 2.144013466,log10 il1 beta (pg/ml): -0.619788758,log10 ogtt fasting plasma insulin (mu/l): 1.1430148,ogtt 30 min plasma insulin (mu/l): 2.033825694,ogtt 120 min plasma insulin (mu/l): 1.691965103,log10 ogtt fasting plasma proinsulin (pm/l): 0.929418926,ogtt 30 min plasma proinsulin (pm/l): 1.392696953,ogtt 120 min plasma proinsulin (pm/l): 1.597695186,log10 bioimpedance: Resistance: 2.697229343,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.921568627,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.361727836,log10 creatinine (umol/l): 1.826074803,log10 total cholesterol (mmol/l): 0.646403726,log10 ldl cholesterol (mmol/l): 0.421603927,log10 hdl cholesterol (mmol/l): 0.11058971,log10 total triglycerides (mmol/l): 0.017033339,log10 serum apoa1 (g/l): 0.103803721,log10 serum apob (g/l): -0.086186148,log10 urinary albumin excretion rate (ug/min): 0.491577171 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098282 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249181,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978109 | GSM1098282 | GSE45159 | 0.146951 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2570 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249181 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978109 |
|
1 | age: 47,tissue: adipose tissue,log10 body mass index: 1.406526027,log10 basal metabolic rate (kcal): 1824,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.4965775,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.835208183,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.25,fat mass (%): 20.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.667111542,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 141,log10 homair (insulin resistance index based on homa): -0.0019345,log10 homais (insulin secretion index based on homa): 1.580870692,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.324014798,insgenin (insulinogenic index): 1.850033258,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.260238392,log10 matsuda insulin sensitivity index: 0.984903437,muscle mass (%): 48.4,lg10 serum c-reactive protein (mg/l): -0.171340103,lg10 plasma adiponectin (mg/l): 0.832508913,ogtt fasting plasma free fatty acid (mmol/l): 0.52,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.1,ogtt 120 min plasma glucose (mmol/l): 5.4,log10 il1 receptor antagonist (pg/ml): 2.190723787,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.602059991,ogtt 30 min plasma insulin (mu/l): 1.525044807,ogtt 120 min plasma insulin (mu/l): 1.506505032,log10 ogtt fasting plasma proinsulin (pm/l): 1.056904851,ogtt 30 min plasma proinsulin (pm/l): 1.397940009,ogtt 120 min plasma proinsulin (pm/l): 1.669316881,log10 bioimpedance: Resistance: 2.696356389,log10 bioimpedance (reactance): 1.826074803,waist to hip ratio: 0.940594059,log10 serum bilirubin (umol/l): 1.278753601,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.698100546,log10 ldl cholesterol (mmol/l): 0.534026106,log10 hdl cholesterol (mmol/l): 0.079181246,log10 total triglycerides (mmol/l): -0.040958608,log10 serum apoa1 (g/l): -0.065501549,log10 serum apob (g/l): -0.148741651,log10 urinary albumin excretion rate (ug/min): 1.189680981 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098283 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249182,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978110 | GSM1098283 | GSE45159 | 0.220173 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2620 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249182 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978110 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.487123549,log10 basal metabolic rate (kcal): 1792,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.414234205,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.036198439,plasma free fatty acids under the curve ogtt (mmol/l * min): 28.65,fat mass (%): 25.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.777255315,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 205.5,log10 homair (insulin resistance index based on homa): 0.506595219,log10 homais (insulin secretion index based on homa): 2.089400411,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.515343893,insgenin (insulinogenic index): 1.770531854,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.370550096,log10 matsuda insulin sensitivity index: 0.599401322,muscle mass (%): 42.4,lg10 serum c-reactive protein (mg/l): -0.056505484,lg10 plasma adiponectin (mg/l): 0.908485019,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.33,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 7.9,ogtt 120 min plasma glucose (mmol/l): 7.1,log10 il1 receptor antagonist (pg/ml): 2.392556268,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.11058971,ogtt 30 min plasma insulin (mu/l): 1.550228353,ogtt 120 min plasma insulin (mu/l): 1.843232778,log10 ogtt fasting plasma proinsulin (pm/l): 1.201397124,ogtt 30 min plasma proinsulin (pm/l): 1.390935107,ogtt 120 min plasma proinsulin (pm/l): 1.851869601,log10 bioimpedance: Resistance: 2.653212514,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 1.037037037,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.680335513,log10 ldl cholesterol (mmol/l): 0.501059262,log10 hdl cholesterol (mmol/l): 0.041392685,log10 total triglycerides (mmol/l): 0.274157849,log10 serum apoa1 (g/l): 0.120573931,log10 serum apob (g/l): 0.025305865,log10 urinary albumin excretion rate (ug/min): 0.808114474 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098284 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249183,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978111 | GSM1098284 | GSE45159 | 0.206903 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2655 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249183 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978111 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.328942923,log10 basal metabolic rate (kcal): 1576,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.874160185,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.681584994,plasma free fatty acids under the curve ogtt (mmol/l * min): 13.8,fat mass (%): 9.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.839991071,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 148.5,log10 homair (insulin resistance index based on homa): -0.040852566,log10 homais (insulin secretion index based on homa): 1.343781976,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.284453294,insgenin (insulinogenic index): 1.815134817,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.229092829,log10 matsuda insulin sensitivity index: 1.015466625,muscle mass (%): 52.7,lg10 serum c-reactive protein (mg/l): -0.278189385,lg10 plasma adiponectin (mg/l): 1.029383778,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.09,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 10,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.130301597,log10 il1 beta (pg/ml): -0.744727495,log10 ogtt fasting plasma insulin (mu/l): 0.505149978,ogtt 30 min plasma insulin (mu/l): 1.627365857,ogtt 120 min plasma insulin (mu/l): 1.136720567,log10 ogtt fasting plasma proinsulin (pm/l): 1.068185862,ogtt 30 min plasma proinsulin (pm/l): 1.536558443,ogtt 120 min plasma proinsulin (pm/l): 1.602059991,log10 bioimpedance: Resistance: 2.661812686,log10 bioimpedance (reactance): 1.707570176,waist to hip ratio: 0.911111111,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.62324929,log10 creatinine (umol/l): 1.819543936,log10 total cholesterol (mmol/l): 0.789580712,log10 ldl cholesterol (mmol/l): 0.357934847,log10 hdl cholesterol (mmol/l): 0.574031268,log10 total triglycerides (mmol/l): -0.337242168,log10 serum apoa1 (g/l): 0.418301291,log10 serum apob (g/l): -0.200659451,log10 urinary albumin excretion rate (ug/min): 0.522579129 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098285 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249184,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978112 | GSM1098285 | GSE45159 | 0.353391 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2656 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249184 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978112 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.482822136,log10 basal metabolic rate (kcal): 1756,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.758382361,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.153855187,plasma free fatty acids under the curve ogtt (mmol/l * min): 34.05,fat mass (%): 23.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.13185696,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 390,log10 homair (insulin resistance index based on homa): 0.428782511,log10 homais (insulin secretion index based on homa): 1.881691842,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.476686743,insgenin (insulinogenic index): 1.364416975,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.358734127,log10 matsuda insulin sensitivity index: 0.616634639,muscle mass (%): 45.8,lg10 serum c-reactive protein (mg/l): 0.08350262,lg10 plasma adiponectin (mg/l): 0.763427994,ogtt fasting plasma free fatty acid (mmol/l): 0.58,ogtt 30 min plasma free fatty acid (mmol/l): 0.4,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.1,ogtt 30 min plasma glucose (mmol/l): 11.7,ogtt 120 min plasma glucose (mmol/l): 7.3,log10 il1 receptor antagonist (pg/ml): 2.309672743,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.995635195,ogtt 30 min plasma insulin (mu/l): 1.498310554,ogtt 120 min plasma insulin (mu/l): 1.81756537,log10 ogtt fasting plasma proinsulin (pm/l): 1.227886705,ogtt 30 min plasma proinsulin (pm/l): 1.426511261,ogtt 120 min plasma proinsulin (pm/l): 1.805500858,log10 bioimpedance: Resistance: 2.63748973,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 1.03960396,log10 serum bilirubin (umol/l): 0.954242509,log10 serum alanine aminotransfrase (u/l): 1.73239376,log10 creatinine (umol/l): 1.851258349,log10 total cholesterol (mmol/l): 0.681241237,log10 ldl cholesterol (mmol/l): 0.474216264,log10 hdl cholesterol (mmol/l): 0.025305865,log10 total triglycerides (mmol/l): 0.164352856,log10 serum apoa1 (g/l): 0.117271296,log10 serum apob (g/l): 0.008600172,log10 urinary albumin excretion rate (ug/min): 1.397940009 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098286 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249185,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978113 | GSM1098286 | GSE45159 | 0.33132 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2687 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249185 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978113 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.440512622,log10 basal metabolic rate (kcal): 2169,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.433481472,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.967569867,plasma free fatty acids under the curve ogtt (mmol/l * min): 27,fat mass (%): 24.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.08081753,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 399,log10 homair (insulin resistance index based on homa): 0.573954053,log10 homais (insulin secretion index based on homa): 2.12886903,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.551498792,insgenin (insulinogenic index): 1.72325038,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.397035735,log10 matsuda insulin sensitivity index: 0.508096077,muscle mass (%): 50.1,lg10 serum c-reactive protein (mg/l): 0.465531557,lg10 plasma adiponectin (mg/l): 0.568201724,ogtt fasting plasma free fatty acid (mmol/l): 0.41,ogtt 30 min plasma free fatty acid (mmol/l): 0.28,ogtt 120 min plasma free fatty acid (mmol/l): 0.09,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 8.9,ogtt 120 min plasma glucose (mmol/l): 10.3,log10 il1 receptor antagonist (pg/ml): 2.719289845,log10 il1 beta (pg/ml): -0.091514981,log10 ogtt fasting plasma insulin (mu/l): 1.170261715,ogtt 30 min plasma insulin (mu/l): 1.633468456,ogtt 120 min plasma insulin (mu/l): 1.84260924,log10 ogtt fasting plasma proinsulin (pm/l): 1.139879086,ogtt 30 min plasma proinsulin (pm/l): 1.439332694,ogtt 120 min plasma proinsulin (pm/l): 1.771587481,log10 bioimpedance: Resistance: 2.698970004,log10 bioimpedance (reactance): 1.963787827,waist to hip ratio: 0.944444444,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 2.045322979,log10 creatinine (umol/l): 1.934498451,log10 total cholesterol (mmol/l): 0.706717782,log10 ldl cholesterol (mmol/l): 0.371067862,log10 hdl cholesterol (mmol/l): 0.294466226,log10 total triglycerides (mmol/l): 0.209515015,log10 serum apoa1 (g/l): 0.281033367,log10 serum apob (g/l): -0.065501549,log10 urinary albumin excretion rate (ug/min): 1.221153322 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098287 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249186,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978114 | GSM1098287 | GSE45159 | 0.197954 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2692 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249186 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978114 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.355258228,log10 basal metabolic rate (kcal): 1786,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.805953314,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.787902468,plasma free fatty acids under the curve ogtt (mmol/l * min): 7.95,fat mass (%): 13.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.285402219,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 48,log10 homair (insulin resistance index based on homa): -0.239577517,log10 homais (insulin secretion index based on homa): 1.618450408,log10 insulin area under the curve (ogtt) (pmol/l * min): 3.865400118,insgenin (insulinogenic index): 1.636344588,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.731669332,log10 matsuda insulin sensitivity index: 1.381152143,muscle mass (%): 54.5,lg10 serum c-reactive protein (mg/l): -0.542118103,lg10 plasma adiponectin (mg/l): 1.1430148,ogtt fasting plasma free fatty acid (mmol/l): 0.23,ogtt 30 min plasma free fatty acid (mmol/l): 0.06,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 4.8,ogtt 30 min plasma glucose (mmol/l): 6.2,ogtt 120 min plasma glucose (mmol/l): 4,log10 il1 receptor antagonist (pg/ml): 1.965765964,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.431363764,ogtt 30 min plasma insulin (mu/l): 1.10720997,ogtt 120 min plasma insulin (mu/l): 0.963787827,log10 ogtt fasting plasma proinsulin (pm/l): 0.740362689,ogtt 30 min plasma proinsulin (pm/l): 0.84509804,ogtt 120 min plasma proinsulin (pm/l): 1.071882007,log10 bioimpedance: Resistance: 2.673941999,log10 bioimpedance (reactance): 1.838849091,waist to hip ratio: 0.804123711,log10 serum bilirubin (umol/l): 0.77815125,log10 serum alanine aminotransfrase (u/l): 1.447158031,log10 creatinine (umol/l): 1.838849091,log10 total cholesterol (mmol/l): 0.725911632,log10 ldl cholesterol (mmol/l): 0.378397901,log10 hdl cholesterol (mmol/l): 0.365487985,log10 total triglycerides (mmol/l): -0.283996656,log10 serum apoa1 (g/l): 0.269512944,log10 serum apob (g/l): -0.187086643,log10 urinary albumin excretion rate (ug/min): 0.948638632 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098288 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249187,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978115 | GSM1098288 | GSE45159 | 0.20599 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2704 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249187 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978115 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.414036229,log10 basal metabolic rate (kcal): 1672,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.466969775,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.666944316,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.05,fat mass (%): 17.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.59058705,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 87,log10 homair (insulin resistance index based on homa): 0.093888418,log10 homais (insulin secretion index based on homa): 1.648803395,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.657619878,insgenin (insulinogenic index): 2.454429068,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.62253522,log10 matsuda insulin sensitivity index: 0.802099391,muscle mass (%): 47.8,lg10 serum c-reactive protein (mg/l): -0.294992041,lg10 plasma adiponectin (mg/l): 0.72427587,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.09,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 7.9,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.140759371,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.69019608,ogtt 30 min plasma insulin (mu/l): 2.038620162,ogtt 120 min plasma insulin (mu/l): 1.322219295,log10 ogtt fasting plasma proinsulin (pm/l): 0.919078092,ogtt 30 min plasma proinsulin (pm/l): 1.519827994,ogtt 120 min plasma proinsulin (pm/l): 1.602059991,log10 bioimpedance: Resistance: 2.633468456,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.942105263,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.683947131,log10 ldl cholesterol (mmol/l): 0.45331834,log10 hdl cholesterol (mmol/l): 0.170261715,log10 total triglycerides (mmol/l): -0.086186148,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): -0.065501549,log10 urinary albumin excretion rate (ug/min): 0.653212514 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098289 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249188,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978116 | GSM1098289 | GSE45159 | 0.04737 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2735 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249188 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978116 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.3285186,log10 basal metabolic rate (kcal): 1525,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.512775985,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.458624917,plasma free fatty acids under the curve ogtt (mmol/l * min): 12.45,fat mass (%): 15.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.509775004,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): -3,log10 homair (insulin resistance index based on homa): 0.056396607,log10 homais (insulin secretion index based on homa): 1.509305938,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.429332313,insgenin (insulinogenic index): 2.25196987,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.377488383,log10 matsuda insulin sensitivity index: 0.946951921,muscle mass (%): 48,lg10 serum c-reactive protein (mg/l): -0.303643611,lg10 plasma adiponectin (mg/l): 0.903089987,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.13,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6.1,ogtt 30 min plasma glucose (mmol/l): 8.3,ogtt 120 min plasma glucose (mmol/l): 3.1,log10 il1 receptor antagonist (pg/ml): 2.171023996,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.62324929,ogtt 30 min plasma insulin (mu/l): 1.843232778,ogtt 120 min plasma insulin (mu/l): 0.716003344,log10 ogtt fasting plasma proinsulin (pm/l): 0.929418926,ogtt 30 min plasma proinsulin (pm/l): 1.527629901,ogtt 120 min plasma proinsulin (pm/l): 1.320146286,log10 bioimpedance: Resistance: 2.757396029,log10 bioimpedance (reactance): 1.792391689,waist to hip ratio: 0.9375,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.77815125,log10 ldl cholesterol (mmol/l): 0.492760389,log10 hdl cholesterol (mmol/l): 0.369215857,log10 total triglycerides (mmol/l): -0.013228266,log10 serum apoa1 (g/l): 0.285557309,log10 serum apob (g/l): -0.036212173,log10 urinary albumin excretion rate (ug/min): 0.763079582 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098290 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249189,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978117 | GSM1098290 | GSE45159 | 0.160218 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2760 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249189 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978117 |
|
1 | age: 49,tissue: adipose tissue,log10 body mass index: 1.446274549,log10 basal metabolic rate (kcal): 1544,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.464670105,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.661239616,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.5,fat mass (%): 21.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.550746785,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 78,log10 homair (insulin resistance index based on homa): 0.2936326,log10 homais (insulin secretion index based on homa): 1.876437792,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.439821986,insgenin (insulinogenic index): 2.021685352,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.339312286,log10 matsuda insulin sensitivity index: 0.797833303,muscle mass (%): 45.9,lg10 serum c-reactive protein (mg/l): 0.651665604,lg10 plasma adiponectin (mg/l): 0.792391689,ogtt fasting plasma free fatty acid (mmol/l): 0.46,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.1,ogtt 120 min plasma glucose (mmol/l): 4,log10 il1 receptor antagonist (pg/ml): 2.207391978,log10 il1 beta (pg/ml): -0.619788758,log10 ogtt fasting plasma insulin (mu/l): 0.897627091,ogtt 30 min plasma insulin (mu/l): 1.713490543,ogtt 120 min plasma insulin (mu/l): 1.482873584,log10 ogtt fasting plasma proinsulin (pm/l): 1.1430148,ogtt 30 min plasma proinsulin (pm/l): 1.456366033,ogtt 120 min plasma proinsulin (pm/l): 1.621176282,log10 bioimpedance: Resistance: 2.677606953,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 0.910891089,log10 serum bilirubin (umol/l): 1.301029996,log10 serum alanine aminotransfrase (u/l): 1.591064607,log10 creatinine (umol/l): 1.929418926,log10 total cholesterol (mmol/l): 0.668385917,log10 ldl cholesterol (mmol/l): 0.472756449,log10 hdl cholesterol (mmol/l): 0.075546961,log10 total triglycerides (mmol/l): -0.017728767,log10 serum apoa1 (g/l): 0.086359831,log10 serum apob (g/l): -0.036212173,log10 urinary albumin excretion rate (ug/min): 0.698970004 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098291 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249190,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978118 | GSM1098291 | GSE45159 | 0.232723 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2775 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249190 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978118 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.455873908,log10 basal metabolic rate (kcal): 1607,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.611832412,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.906546965,plasma free fatty acids under the curve ogtt (mmol/l * min): 26.55,fat mass (%): 20.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.946906274,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 315,log10 homair (insulin resistance index based on homa): 0.325424435,log10 homais (insulin secretion index based on homa): 1.908229627,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.531504463,insgenin (insulinogenic index): 1.837588438,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.445323923,log10 matsuda insulin sensitivity index: 0.669428844,muscle mass (%): 44.4,lg10 serum c-reactive protein (mg/l): 0.108903128,lg10 plasma adiponectin (mg/l): 0.897627091,ogtt fasting plasma free fatty acid (mmol/l): 0.35,ogtt 30 min plasma free fatty acid (mmol/l): 0.28,ogtt 120 min plasma free fatty acid (mmol/l): 0.1,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.6,ogtt 120 min plasma glucose (mmol/l): 8.6,log10 il1 receptor antagonist (pg/ml): 2.34190912,log10 il1 beta (pg/ml): -0.251811973,log10 ogtt fasting plasma insulin (mu/l): 0.929418926,ogtt 30 min plasma insulin (mu/l): 1.632457292,ogtt 120 min plasma insulin (mu/l): 1.818885415,log10 ogtt fasting plasma proinsulin (pm/l): 0.991226076,ogtt 30 min plasma proinsulin (pm/l): 1.320146286,ogtt 120 min plasma proinsulin (pm/l): 1.668385917,log10 bioimpedance: Resistance: 2.633468456,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 1.030612245,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.62324929,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.78604121,log10 ldl cholesterol (mmol/l): 0.624282096,log10 hdl cholesterol (mmol/l): 0.176091259,log10 total triglycerides (mmol/l): 0.093421685,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): 0.049218023,log10 urinary albumin excretion rate (ug/min): 0.819543936 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098292 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249191,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978119 | GSM1098292 | GSE45159 | 0.239382 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2786 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249191 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978119 |
|
1 | age: 49,tissue: adipose tissue,log10 body mass index: 1.376735503,log10 basal metabolic rate (kcal): 1506,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.811870022,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.782782396,plasma free fatty acids under the curve ogtt (mmol/l * min): 12,fat mass (%): 17.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.436711542,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 9,log10 homair (insulin resistance index based on homa): 0.174544349,log10 homais (insulin secretion index based on homa): 1.729459326,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.367038938,insgenin (insulinogenic index): 2.354108439,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.279552881,log10 matsuda insulin sensitivity index: 0.900297685,muscle mass (%): 47.7,lg10 serum c-reactive protein (mg/l): 0.366796383,lg10 plasma adiponectin (mg/l): 1.017033339,ogtt fasting plasma free fatty acid (mmol/l): 0.26,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 6.6,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.50847585,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.770852012,ogtt 30 min plasma insulin (mu/l): 1.599883072,ogtt 120 min plasma insulin (mu/l): 1.494154594,log10 ogtt fasting plasma proinsulin (pm/l): 1.071882007,ogtt 30 min plasma proinsulin (pm/l): 1.491361694,ogtt 120 min plasma proinsulin (pm/l): 1.687528961,log10 bioimpedance: Resistance: 2.715167358,log10 bioimpedance (reactance): 1.77815125,waist to hip ratio: 0.956989247,log10 serum bilirubin (umol/l): 1.322219295,log10 serum alanine aminotransfrase (u/l): 1.447158031,log10 creatinine (umol/l): 1.838849091,log10 total cholesterol (mmol/l): 0.674861141,log10 ldl cholesterol (mmol/l): 0.51054501,log10 hdl cholesterol (mmol/l): 0.120573931,log10 total triglycerides (mmol/l): 0.08278537,log10 serum apoa1 (g/l): 0.136720567,log10 serum apob (g/l): 0.012837225,log10 urinary albumin excretion rate (ug/min): 1.081621109 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098293 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249192,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978120 | GSM1098293 | GSE45159 | 0.254863 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2869 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249192 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978120 |
|
1 | age: 49,tissue: adipose tissue,log10 body mass index: 1.41701389,log10 basal metabolic rate (kcal): 1634,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.406923157,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.666340488,plasma free fatty acids under the curve ogtt (mmol/l * min): 31.35,fat mass (%): 19.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.772314574,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 310.5,log10 homair (insulin resistance index based on homa): -0.202963405,log10 homais (insulin secretion index based on homa): 1.698970004,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.29666519,insgenin (insulinogenic index): 1.733629307,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.246498581,log10 matsuda insulin sensitivity index: 1.101718914,muscle mass (%): 46.2,lg10 serum c-reactive protein (mg/l): 0.445292769,lg10 plasma adiponectin (mg/l): 0.633468456,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.39,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 4.7,ogtt 30 min plasma glucose (mmol/l): 8.6,ogtt 120 min plasma glucose (mmol/l): 6.4,log10 il1 receptor antagonist (pg/ml): 2.219139002,log10 il1 beta (pg/ml): 0.371067862,log10 ogtt fasting plasma insulin (mu/l): 0.477121255,ogtt 30 min plasma insulin (mu/l): 1.582063363,ogtt 120 min plasma insulin (mu/l): 1.330413773,log10 ogtt fasting plasma proinsulin (pm/l): 0.954242509,ogtt 30 min plasma proinsulin (pm/l): 1.184691431,ogtt 120 min plasma proinsulin (pm/l): 1.484299839,log10 bioimpedance: Resistance: 2.679427897,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.93877551,log10 serum bilirubin (umol/l): 1.447158031,log10 serum alanine aminotransfrase (u/l): 1.556302501,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.667452953,log10 ldl cholesterol (mmol/l): 0.492760389,log10 hdl cholesterol (mmol/l): 0.071882007,log10 total triglycerides (mmol/l): -0.187086643,log10 serum apoa1 (g/l): 0.10720997,log10 serum apob (g/l): -0.040958608,log10 urinary albumin excretion rate (ug/min): 0.73488256 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098294 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249193,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978121 | GSM1098294 | GSE45159 | 0.081794 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2950 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249193 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978121 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.409302874,log10 basal metabolic rate (kcal): 1599,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.032070299,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.082059391,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.15,fat mass (%): 15.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.274960472,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 7.5,log10 homair (insulin resistance index based on homa): -0.076410618,log10 homais (insulin secretion index based on homa): 1.665111737,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.224455364,insgenin (insulinogenic index): 2.129765692,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.149311506,log10 matsuda insulin sensitivity index: 1.145294407,muscle mass (%): 49.4,lg10 serum c-reactive protein (mg/l): -0.493494968,lg10 plasma adiponectin (mg/l): 0.982271233,ogtt fasting plasma free fatty acid (mmol/l): 0.29,ogtt 30 min plasma free fatty acid (mmol/l): 0.15,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.1,ogtt 30 min plasma glucose (mmol/l): 6.8,ogtt 120 min plasma glucose (mmol/l): 3,log10 il1 receptor antagonist (pg/ml): 1.491361694,log10 il1 beta (pg/ml): -0.769551079,log10 ogtt fasting plasma insulin (mu/l): 0.568201724,ogtt 30 min plasma insulin (mu/l): 1.622214023,ogtt 120 min plasma insulin (mu/l): 0.698970004,log10 ogtt fasting plasma proinsulin (pm/l): 0.929418926,ogtt 30 min plasma proinsulin (pm/l): 1.45331834,ogtt 120 min plasma proinsulin (pm/l): 1.36361198,log10 bioimpedance: Resistance: 2.621176282,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 0.924731183,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 2.029383778,log10 total cholesterol (mmol/l): 0.720985744,log10 ldl cholesterol (mmol/l): 0.514547753,log10 hdl cholesterol (mmol/l): 0.184691431,log10 total triglycerides (mmol/l): 0.045322979,log10 serum apoa1 (g/l): 0.212187604,log10 serum apob (g/l): -0.008773924,log10 urinary albumin excretion rate (ug/min): 0.438724864 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098295 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249194,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978122 | GSM1098295 | GSE45159 | 0 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM3923 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249194 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978122 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.394794611,log10 basal metabolic rate (kcal): 1503,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.601614851,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.595498422,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.55,fat mass (%): 19.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.727069558,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 199.5,log10 homair (insulin resistance index based on homa): 0.151063253,log10 homais (insulin secretion index based on homa): 1.793128406,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.422737534,insgenin (insulinogenic index): 1.863672674,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.346763599,log10 matsuda insulin sensitivity index: 0.857454925,muscle mass (%): 45.4,lg10 serum c-reactive protein (mg/l): -0.539102157,lg10 plasma adiponectin (mg/l): 0.748188027,ogtt fasting plasma free fatty acid (mmol/l): 0.27,ogtt 30 min plasma free fatty acid (mmol/l): 0.23,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 8.8,ogtt 120 min plasma glucose (mmol/l): 5.3,log10 il1 receptor antagonist (pg/ml): 2.296709056,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.770852012,ogtt 30 min plasma insulin (mu/l): 1.674861141,ogtt 120 min plasma insulin (mu/l): 1.51851394,log10 ogtt fasting plasma proinsulin (pm/l): 1.225309282,ogtt 30 min plasma proinsulin (pm/l): 1.609594409,ogtt 120 min plasma proinsulin (pm/l): 1.746634199,log10 bioimpedance: Resistance: 2.728353782,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 0.918367347,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.880813592,log10 total cholesterol (mmol/l): 0.820201459,log10 ldl cholesterol (mmol/l): 0.689308859,log10 hdl cholesterol (mmol/l): 0.220108088,log10 total triglycerides (mmol/l): 0.049218023,log10 serum apoa1 (g/l): 0.176091259,log10 serum apob (g/l): 0.117271296,log10 urinary albumin excretion rate (ug/min): 0.78612018 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098296 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249195,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978123 | GSM1098296 | GSE45159 | 0.297953 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4137 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249195 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978123 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.486234644,log10 basal metabolic rate (kcal): 1571,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.663659264,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.897285928,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.3,fat mass (%): 23.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.33315535,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 498,log10 homair (insulin resistance index based on homa): 0.819543936,log10 homais (insulin secretion index based on homa): 2.16185082,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.84011237,insgenin (insulinogenic index): 1.951753709,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.724284064,log10 matsuda insulin sensitivity index: 0.203786946,muscle mass (%): 43.4,lg10 serum c-reactive protein (mg/l): 0.899765802,lg10 plasma adiponectin (mg/l): 0.698970004,ogtt fasting plasma free fatty acid (mmol/l): 0.18,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 6.6,ogtt 30 min plasma glucose (mmol/l): 10.1,ogtt 120 min plasma glucose (mmol/l): 13,log10 il1 receptor antagonist (pg/ml): 2.173565018,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.352182518,ogtt 30 min plasma insulin (mu/l): 1.873320602,ogtt 120 min plasma insulin (mu/l): 2.173768823,log10 ogtt fasting plasma proinsulin (pm/l): 1.029383778,ogtt 30 min plasma proinsulin (pm/l): 1.178976947,ogtt 120 min plasma proinsulin (pm/l): 1.559906625,log10 bioimpedance: Resistance: 2.641474111,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 1.025,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.342422681,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.73239376,log10 ldl cholesterol (mmol/l): 0.602059991,log10 hdl cholesterol (mmol/l): -0.107905397,log10 total triglycerides (mmol/l): 0.354108439,log10 serum apoa1 (g/l): 0.012837225,log10 serum apob (g/l): 0.155336037,log10 urinary albumin excretion rate (ug/min): 0.706188361 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098297 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249196,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978124 | GSM1098297 | GSE45159 | 0.162635 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4245 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249196 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978124 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.40910345,log10 basal metabolic rate (kcal): 1608,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.826563739,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.974462784,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.25,fat mass (%): 20.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.45532722,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 42,log10 homair (insulin resistance index based on homa): 0.050938003,log10 homais (insulin secretion index based on homa): 1.662757832,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.31160554,insgenin (insulinogenic index): 1.939519253,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.235048438,log10 matsuda insulin sensitivity index: 0.984728748,muscle mass (%): 43.8,lg10 serum c-reactive protein (mg/l): 0.341236623,lg10 plasma adiponectin (mg/l): 1.127104798,ogtt fasting plasma free fatty acid (mmol/l): 0.35,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 7.1,ogtt 120 min plasma glucose (mmol/l): 4.3,log10 il1 receptor antagonist (pg/ml): 2.152380087,log10 il1 beta (pg/ml): -0.397940009,log10 ogtt fasting plasma insulin (mu/l): 0.662757832,ogtt 30 min plasma insulin (mu/l): 1.444044796,ogtt 120 min plasma insulin (mu/l): 1.571708832,log10 ogtt fasting plasma proinsulin (pm/l): 1.06069784,ogtt 30 min plasma proinsulin (pm/l): 1.294466226,ogtt 120 min plasma proinsulin (pm/l): 1.660865478,log10 bioimpedance: Resistance: 2.683947131,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 1.077720207,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.531478917,log10 creatinine (umol/l): 1.819543936,log10 total cholesterol (mmol/l): 0.791690649,log10 ldl cholesterol (mmol/l): 0.436162647,log10 hdl cholesterol (mmol/l): 0.562292864,log10 total triglycerides (mmol/l): -0.187086643,log10 serum apoa1 (g/l): 0.385606274,log10 serum apob (g/l): -0.207608311,log10 urinary albumin excretion rate (ug/min): 1.190731785 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098298 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249197,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978125 | GSM1098298 | GSE45159 | 0.170863 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4257 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249197 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978125 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.407891767,log10 basal metabolic rate (kcal): 1564,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.176694037,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.378411341,plasma free fatty acids under the curve ogtt (mmol/l * min): 25.8,fat mass (%): 19.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.801708359,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 232.5,log10 homair (insulin resistance index based on homa): 0.050938003,log10 homais (insulin secretion index based on homa): 1.662757832,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.416640507,insgenin (insulinogenic index): 1.692522248,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.357706211,log10 matsuda insulin sensitivity index: 0.893726147,muscle mass (%): 45.6,lg10 serum c-reactive protein (mg/l): -0.274905479,lg10 plasma adiponectin (mg/l): 0.826074803,ogtt fasting plasma free fatty acid (mmol/l): 0.42,ogtt 30 min plasma free fatty acid (mmol/l): 0.28,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 5.6,log10 il1 receptor antagonist (pg/ml): 2.142264291,log10 il1 beta (pg/ml): -0.161150909,log10 ogtt fasting plasma insulin (mu/l): 0.662757832,ogtt 30 min plasma insulin (mu/l): 1.553883027,ogtt 120 min plasma insulin (mu/l): 1.675778342,log10 ogtt fasting plasma proinsulin (pm/l): 0.963787827,ogtt 30 min plasma proinsulin (pm/l): 1.330413773,ogtt 120 min plasma proinsulin (pm/l): 1.727541257,log10 bioimpedance: Resistance: 2.698100546,log10 bioimpedance (reactance): 1.740362689,waist to hip ratio: 0.955445545,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 2,log10 total cholesterol (mmol/l): 0.689308859,log10 ldl cholesterol (mmol/l): 0.525044807,log10 hdl cholesterol (mmol/l): 0.184691431,log10 total triglycerides (mmol/l): -0.017728767,log10 serum apoa1 (g/l): 0.123851641,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 0.897486109 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098299 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249198,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978126 | GSM1098299 | GSE45159 | 0.325016 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4336 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249198 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978126 |
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1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.370268582,log10 basal metabolic rate (kcal): 1673,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.052998278,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.228774653,plasma free fatty acids under the curve ogtt (mmol/l * min): 14.4,fat mass (%): 15.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.714245518,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 192,log10 homair (insulin resistance index based on homa): -0.040005162,log10 homais (insulin secretion index based on homa): 1.602059991,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.265572462,insgenin (insulinogenic index): 1.781479194,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.19578899,log10 matsuda insulin sensitivity index: 1.027680246,muscle mass (%): 48.2,lg10 serum c-reactive protein (mg/l): 0.375846436,lg10 plasma adiponectin (mg/l): 0.903089987,ogtt fasting plasma free fatty acid (mmol/l): 0.23,ogtt 30 min plasma free fatty acid (mmol/l): 0.16,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 8,ogtt 120 min plasma glucose (mmol/l): 6.2,log10 il1 receptor antagonist (pg/ml): 1.996248915,log10 il1 beta (pg/ml): -0.283996656,log10 ogtt fasting plasma insulin (mu/l): 0.579783597,ogtt 30 min plasma insulin (mu/l): 1.477121255,ogtt 120 min plasma insulin (mu/l): 1.431363764,log10 ogtt fasting plasma proinsulin (pm/l): 0.806179974,ogtt 30 min plasma proinsulin (pm/l): 1.11058971,ogtt 120 min plasma proinsulin (pm/l): 1.278753601,log10 bioimpedance: Resistance: 2.669316881,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 0.911458333,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.380211242,log10 creatinine (umol/l): 2.029383778,log10 total cholesterol (mmol/l): 0.866877814,log10 ldl cholesterol (mmol/l): 0.728353782,log10 hdl cholesterol (mmol/l): 0.250420002,log10 total triglycerides (mmol/l): 0.029383778,log10 serum apoa1 (g/l): 0.152288344,log10 serum apob (g/l): 0.096910013,log10 urinary albumin excretion rate (ug/min): 0.948847478 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098300 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249199,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978127 | GSM1098300 | GSE45159 | 0.173202 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4403 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249199 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978127 |
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1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.49138949,log10 basal metabolic rate (kcal): 1426,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.347610464,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.60975696,plasma free fatty acids under the curve ogtt (mmol/l * min): 27.45,fat mass (%): 26.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.794415866,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 216,log10 homair (insulin resistance index based on homa): 0.103575685,log10 homais (insulin secretion index based on homa): 1.686380877,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.560516363,insgenin (insulinogenic index): 2.112456041,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.514268758,log10 matsuda insulin sensitivity index: 0.80207722,muscle mass (%): 40,lg10 serum c-reactive protein (mg/l): 0.763877031,lg10 plasma adiponectin (mg/l): 0.556302501,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.32,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.3,ogtt 120 min plasma glucose (mmol/l): 6.8,log10 il1 receptor antagonist (pg/ml): 2.647940153,log10 il1 beta (pg/ml): -0.568636236,log10 ogtt fasting plasma insulin (mu/l): 0.707570176,ogtt 30 min plasma insulin (mu/l): 1.802089258,ogtt 120 min plasma insulin (mu/l): 1.684845362,log10 ogtt fasting plasma proinsulin (pm/l): 1.053078443,ogtt 30 min plasma proinsulin (pm/l): 1.426511261,ogtt 120 min plasma proinsulin (pm/l): 1.649334859,log10 bioimpedance: Resistance: 2.711807229,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.95412844,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.505149978,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.822821645,log10 ldl cholesterol (mmol/l): 0.681241237,log10 hdl cholesterol (mmol/l): 0.079181246,log10 total triglycerides (mmol/l): 0.181843588,log10 serum apoa1 (g/l): 0.045322979,log10 serum apob (g/l): 0.103803721,log10 urinary albumin excretion rate (ug/min): 0.654996067 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098301 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249200,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978128 | GSM1098301 | GSE45159 | 0.297377 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4485 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249200 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978128 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.470991004,log10 basal metabolic rate (kcal): 1545,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.390807277,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.652578116,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.95,fat mass (%): 21.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.744833837,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 282,log10 homair (insulin resistance index based on homa): 0.16790781,log10 homais (insulin secretion index based on homa): 2.025935734,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.385606274,insgenin (insulinogenic index): 1.815367995,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.286276786,log10 matsuda insulin sensitivity index: 0.870467892,muscle mass (%): 42.8,lg10 serum c-reactive protein (mg/l): 0.183839037,lg10 plasma adiponectin (mg/l): 0.812913357,ogtt fasting plasma free fatty acid (mmol/l): 0.4,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 4.8,ogtt 30 min plasma glucose (mmol/l): 8.6,ogtt 120 min plasma glucose (mmol/l): 6,log10 il1 receptor antagonist (pg/ml): 1.994405147,log10 il1 beta (pg/ml): -0.853871964,log10 ogtt fasting plasma insulin (mu/l): 0.838849091,ogtt 30 min plasma insulin (mu/l): 1.683947131,ogtt 120 min plasma insulin (mu/l): 1.367355921,log10 ogtt fasting plasma proinsulin (pm/l): 0.924279286,ogtt 30 min plasma proinsulin (pm/l): 1.164352856,ogtt 120 min plasma proinsulin (pm/l): 1.338456494,log10 bioimpedance: Resistance: 2.633468456,log10 bioimpedance (reactance): 1.612783857,waist to hip ratio: 1.009803922,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.414973348,log10 creatinine (umol/l): 1.934498451,log10 total cholesterol (mmol/l): 0.629409599,log10 ldl cholesterol (mmol/l): 0.36361198,log10 hdl cholesterol (mmol/l): 0.217483944,log10 total triglycerides (mmol/l): 0.11058971,log10 serum apoa1 (g/l): 0.170261715,log10 serum apob (g/l): -0.091514981,log10 urinary albumin excretion rate (ug/min): 0.802723434 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098302 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249201,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978129 | GSM1098302 | GSE45159 | 0.198207 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4542 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249201 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978129 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.425259611,log10 basal metabolic rate (kcal): 1542,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.485385281,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.688366794,plasma free fatty acids under the curve ogtt (mmol/l * min): 21.9,fat mass (%): 19.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.23959853,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 561,log10 homair (insulin resistance index based on homa): 0.199755177,log10 homais (insulin secretion index based on homa): 1.84182033,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.50776145,insgenin (insulinogenic index): 1.562590225,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.438399934,log10 matsuda insulin sensitivity index: 0.727385358,muscle mass (%): 43.7,lg10 serum c-reactive protein (mg/l): -0.017728767,lg10 plasma adiponectin (mg/l): 0.62324929,ogtt fasting plasma free fatty acid (mmol/l): 0.37,ogtt 30 min plasma free fatty acid (mmol/l): 0.25,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 13.4,ogtt 120 min plasma glucose (mmol/l): 7.2,log10 il1 receptor antagonist (pg/ml): 1.767304317,log10 il1 beta (pg/ml): -0.677780705,log10 ogtt fasting plasma insulin (mu/l): 0.819543936,ogtt 30 min plasma insulin (mu/l): 1.742725131,ogtt 120 min plasma insulin (mu/l): 1.636487896,log10 ogtt fasting plasma proinsulin (pm/l): 1.004321374,ogtt 30 min plasma proinsulin (pm/l): 1.201397124,ogtt 120 min plasma proinsulin (pm/l): 1.487138375,log10 bioimpedance: Resistance: 2.658964843,log10 bioimpedance (reactance): 1.612783857,waist to hip ratio: 0.933333333,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.693726949,log10 ldl cholesterol (mmol/l): 0.544068044,log10 hdl cholesterol (mmol/l): -0.008773924,log10 total triglycerides (mmol/l): 0.201397124,log10 serum apoa1 (g/l): 0.056904851,log10 serum apob (g/l): 0.053078443,log10 urinary albumin excretion rate (ug/min): 1.06694679 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098303 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249202,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978130 | GSM1098303 | GSE45159 | 0.058284 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4572 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249202 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978130 |
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1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.45592839,log10 basal metabolic rate (kcal): 1636,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.22018118,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.491065354,plasma free fatty acids under the curve ogtt (mmol/l * min): 26.4,fat mass (%): 31.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.847057346,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 261,log10 homair (insulin resistance index based on homa): 0.220689084,log10 homais (insulin secretion index based on homa): 1.832508913,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.58334616,insgenin (insulinogenic index): 1.951262776,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.523967459,log10 matsuda insulin sensitivity index: 0.726196008,muscle mass (%): 43.7,lg10 serum c-reactive protein (mg/l): -0.003050752,lg10 plasma adiponectin (mg/l): 0.672097858,ogtt fasting plasma free fatty acid (mmol/l): 0.35,ogtt 30 min plasma free fatty acid (mmol/l): 0.3,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 9.4,ogtt 120 min plasma glucose (mmol/l): 6.1,log10 il1 receptor antagonist (pg/ml): 2.425974161,log10 il1 beta (pg/ml): -0.443697499,log10 ogtt fasting plasma insulin (mu/l): 0.832508913,ogtt 30 min plasma insulin (mu/l): 1.812244697,ogtt 120 min plasma insulin (mu/l): 1.725094521,log10 ogtt fasting plasma proinsulin (pm/l): 1.173186268,ogtt 30 min plasma proinsulin (pm/l): 1.557507202,ogtt 120 min plasma proinsulin (pm/l): 1.814913181,log10 bioimpedance: Resistance: 2.656098202,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.971153846,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 0.954242509,log10 creatinine (umol/l): 1.977723605,log10 total cholesterol (mmol/l): 0.761175813,log10 ldl cholesterol (mmol/l): 0.572871602,log10 hdl cholesterol (mmol/l): 0.220108088,log10 total triglycerides (mmol/l): 0.23299611,log10 serum apoa1 (g/l): 0.212187604,log10 serum apob (g/l): 0.064457989,log10 urinary albumin excretion rate (ug/min): 0.67815016 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098304 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249203,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978131 | GSM1098304 | GSE45159 | 0.188105 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4644 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249203 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978131 |
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1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.392259351,log10 basal metabolic rate (kcal): 1454,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.465179539,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.508352975,plasma free fatty acids under the curve ogtt (mmol/l * min): 31.65,fat mass (%): 21.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.63481105,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 171,log10 homair (insulin resistance index based on homa): 0.277634678,log10 homais (insulin secretion index based on homa): 1.984394927,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.46478752,insgenin (insulinogenic index): 1.941180037,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.366535019,log10 matsuda insulin sensitivity index: 0.765561141,muscle mass (%): 42.8,lg10 serum c-reactive protein (mg/l): 0.144262774,lg10 plasma adiponectin (mg/l): 0.698970004,ogtt fasting plasma free fatty acid (mmol/l): 0.32,ogtt 30 min plasma free fatty acid (mmol/l): 0.38,ogtt 120 min plasma free fatty acid (mmol/l): 0.09,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 7,ogtt 120 min plasma glucose (mmol/l): 6.6,log10 il1 receptor antagonist (pg/ml): 1.966376423,log10 il1 beta (pg/ml): -0.602059991,log10 ogtt fasting plasma insulin (mu/l): 0.913813852,ogtt 30 min plasma insulin (mu/l): 1.536558443,ogtt 120 min plasma insulin (mu/l): 1.773786445,log10 ogtt fasting plasma proinsulin (pm/l): 1.274157849,ogtt 30 min plasma proinsulin (pm/l): 1.434568904,ogtt 120 min plasma proinsulin (pm/l): 1.765668555,log10 bioimpedance: Resistance: 2.754348336,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.951456311,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.733197265,log10 ldl cholesterol (mmol/l): 0.540329475,log10 hdl cholesterol (mmol/l): 0.113943352,log10 total triglycerides (mmol/l): 0.29666519,log10 serum apoa1 (g/l): 0.120573931,log10 serum apob (g/l): 0.06069784,log10 urinary albumin excretion rate (ug/min): 1.098925304 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098305 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249204,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978132 | GSM1098305 | GSE45159 | 0.010244 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4951 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249204 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978132 |
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1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.484090479,log10 basal metabolic rate (kcal): 1524,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.574845136,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.752817126,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.6,fat mass (%): 21,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.1792871,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 307.5,log10 homair (insulin resistance index based on homa): 0.716559775,log10 homais (insulin secretion index based on homa): 1.962211439,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.744738786,insgenin (insulinogenic index): 2.098679036,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.640252801,log10 matsuda insulin sensitivity index: 0.351745386,muscle mass (%): 44,lg10 serum c-reactive protein (mg/l): 0.26245109,lg10 plasma adiponectin (mg/l): 0.491361694,ogtt fasting plasma free fatty acid (mmol/l): 0.28,ogtt 30 min plasma free fatty acid (mmol/l): 0.16,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 7.1,ogtt 30 min plasma glucose (mmol/l): 12,ogtt 120 min plasma glucose (mmol/l): 7.4,log10 il1 receptor antagonist (pg/ml): 2.192316505,log10 il1 beta (pg/ml): 0.643452676,log10 ogtt fasting plasma insulin (mu/l): 1.217483944,ogtt 30 min plasma insulin (mu/l): 2.075546961,ogtt 120 min plasma insulin (mu/l): 1.619093331,log10 ogtt fasting plasma proinsulin (pm/l): 1.432969291,ogtt 30 min plasma proinsulin (pm/l): 1.748962861,ogtt 120 min plasma proinsulin (pm/l): 1.84260924,log10 bioimpedance: Resistance: 2.604226053,log10 bioimpedance (reactance): 1.612783857,waist to hip ratio: 0.950248756,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.568201724,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.743509765,log10 ldl cholesterol (mmol/l): 0.550228353,log10 hdl cholesterol (mmol/l): 0.064457989,log10 total triglycerides (mmol/l): 0.403120521,log10 serum apoa1 (g/l): 0.041392685,log10 serum apob (g/l): 0.06069784,log10 urinary albumin excretion rate (ug/min): 1.691706671 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098306 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249205,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978133 | GSM1098306 | GSE45159 | 0.22924 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM4990 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249205 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978133 |
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1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.406713933,log10 basal metabolic rate (kcal): 1615,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.291799537,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.511062263,plasma free fatty acids under the curve ogtt (mmol/l * min): 18,fat mass (%): 19.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.637530552,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 112.5,log10 homair (insulin resistance index based on homa): 0.167120331,log10 homais (insulin secretion index based on homa): 1.722035308,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.192288613,insgenin (insulinogenic index): 1.784311559,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.056676215,log10 matsuda insulin sensitivity index: 0.963886771,muscle mass (%): 43.9,lg10 serum c-reactive protein (mg/l): 0.881441722,lg10 plasma adiponectin (mg/l): 0.716003344,ogtt fasting plasma free fatty acid (mmol/l): 0.33,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 7.8,ogtt 120 min plasma glucose (mmol/l): 5.4,log10 il1 receptor antagonist (pg/ml): 1.920436407,log10 il1 beta (pg/ml): -0.236572006,log10 ogtt fasting plasma insulin (mu/l): 0.763427994,ogtt 30 min plasma insulin (mu/l): 1.432969291,ogtt 120 min plasma insulin (mu/l): 1.292256071,log10 ogtt fasting plasma proinsulin (pm/l): 0.929418926,ogtt 30 min plasma proinsulin (pm/l): 1.222716471,ogtt 120 min plasma proinsulin (pm/l): 1.556302501,log10 bioimpedance: Resistance: 2.683947131,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 0.889447236,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.204119983,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.790285164,log10 ldl cholesterol (mmol/l): 0.635483747,log10 hdl cholesterol (mmol/l): 0.149219113,log10 total triglycerides (mmol/l): 0.08278537,log10 serum apoa1 (g/l): 0.100370545,log10 serum apob (g/l): 0.117271296,log10 urinary albumin excretion rate (ug/min): 0.716003344 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098307 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249206,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978134 | GSM1098307 | GSE45159 | 0.323388 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5015 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249206 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978134 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.424697384,log10 basal metabolic rate (kcal): 1474,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.470101791,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.609264248,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.9,fat mass (%): 23.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.547858506,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 76.5,log10 homair (insulin resistance index based on homa): 0.241103549,log10 homais (insulin secretion index based on homa): 1.823908741,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.469453814,insgenin (insulinogenic index): 2.228400359,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.388012343,log10 matsuda insulin sensitivity index: 0.803289985,muscle mass (%): 42.1,lg10 serum c-reactive protein (mg/l): 0.05804623,lg10 plasma adiponectin (mg/l): 0.806179974,ogtt fasting plasma free fatty acid (mmol/l): 0.23,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 7.1,ogtt 120 min plasma glucose (mmol/l): 5.3,log10 il1 receptor antagonist (pg/ml): 2.286119503,log10 il1 beta (pg/ml): -0.522878745,log10 ogtt fasting plasma insulin (mu/l): 0.84509804,ogtt 30 min plasma insulin (mu/l): 1.692846919,ogtt 120 min plasma insulin (mu/l): 1.613841822,log10 ogtt fasting plasma proinsulin (pm/l): 1.096910013,ogtt 30 min plasma proinsulin (pm/l): 1.271841607,ogtt 120 min plasma proinsulin (pm/l): 1.547774705,log10 bioimpedance: Resistance: 2.755874856,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 0.971698113,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.301029996,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.660865478,log10 ldl cholesterol (mmol/l): 0.413299764,log10 hdl cholesterol (mmol/l): 0.173186268,log10 total triglycerides (mmol/l): -0.102372909,log10 serum apoa1 (g/l): 0.133538908,log10 serum apob (g/l): -0.119186408,log10 urinary albumin excretion rate (ug/min): 0.772883254 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098308 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249207,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978135 | GSM1098308 | GSE45159 | 0.134585 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5157 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249207 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978135 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.390489841,log10 basal metabolic rate (kcal): 1710,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.376566407,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.265940316,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.1,fat mass (%): 15.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.767356854,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 199.5,log10 homair (insulin resistance index based on homa): 0.144193536,log10 homais (insulin secretion index based on homa): 1.726998728,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.545863548,insgenin (insulinogenic index): 2.039414119,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.492941889,log10 matsuda insulin sensitivity index: 0.808126333,muscle mass (%): 54.9,lg10 serum c-reactive protein (mg/l): 0.112939976,lg10 plasma adiponectin (mg/l): 0.643452676,ogtt fasting plasma free fatty acid (mmol/l): 0.24,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9.6,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 1.831293744,log10 il1 beta (pg/ml): -0.958607315,log10 ogtt fasting plasma insulin (mu/l): 0.748188027,ogtt 30 min plasma insulin (mu/l): 1.895422546,ogtt 120 min plasma insulin (mu/l): 1.371067862,log10 ogtt fasting plasma proinsulin (pm/l): 0.995635195,ogtt 30 min plasma proinsulin (pm/l): 1.465382851,ogtt 120 min plasma proinsulin (pm/l): 1.539076099,log10 bioimpedance: Resistance: 2.666517981,log10 bioimpedance (reactance): 1.897627091,waist to hip ratio: 0.925531915,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.764922985,log10 ldl cholesterol (mmol/l): 0.56937391,log10 hdl cholesterol (mmol/l): 0.274157849,log10 total triglycerides (mmol/l): -0.096910013,log10 serum apoa1 (g/l): 0.198657087,log10 serum apob (g/l): 0.017033339,log10 urinary albumin excretion rate (ug/min): 0.748188027 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098309 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249208,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978136 | GSM1098309 | GSE45159 | 0.326265 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5203 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249208 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978136 |
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1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.468462359,log10 basal metabolic rate (kcal): 1542,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.656291109,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.921856925,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.8,fat mass (%): 24.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.906890596,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 216,log10 homair (insulin resistance index based on homa): 0.547419141,log10 homais (insulin secretion index based on homa): 1.976876201,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.802801082,insgenin (insulinogenic index): 2.189566871,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.734703842,log10 matsuda insulin sensitivity index: 0.435651372,muscle mass (%): 42.3,lg10 serum c-reactive protein (mg/l): 0.386677284,lg10 plasma adiponectin (mg/l): 0.792391689,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.28,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.2,ogtt 30 min plasma glucose (mmol/l): 9.5,ogtt 120 min plasma glucose (mmol/l): 6.6,log10 il1 receptor antagonist (pg/ml): 2.015527404,log10 il1 beta (pg/ml): -0.920818754,log10 ogtt fasting plasma insulin (mu/l): 1.10720997,ogtt 30 min plasma insulin (mu/l): 1.990782692,ogtt 120 min plasma insulin (mu/l): 2.001733713,log10 ogtt fasting plasma proinsulin (pm/l): 1.247973266,ogtt 30 min plasma proinsulin (pm/l): 1.606381365,ogtt 120 min plasma proinsulin (pm/l): 1.859138297,log10 bioimpedance: Resistance: 2.700703717,log10 bioimpedance (reactance): 1.740362689,waist to hip ratio: 1,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 0.84509804,log10 creatinine (umol/l): 1.86923172,log10 total cholesterol (mmol/l): 0.816903839,log10 ldl cholesterol (mmol/l): 0.615950052,log10 hdl cholesterol (mmol/l): 0.195899652,log10 total triglycerides (mmol/l): 0.252853031,log10 serum apoa1 (g/l): 0.086359831,log10 serum apob (g/l): -0.013228266,log10 urinary albumin excretion rate (ug/min): 1.935924869 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098310 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249209,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978137 | GSM1098310 | GSE45159 | 0.241653 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5263 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249209 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978137 |
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1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.444580608,log10 basal metabolic rate (kcal): 1492,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.56346251,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.585358929,plasma free fatty acids under the curve ogtt (mmol/l * min): 12,fat mass (%): 19.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.942514505,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 312,log10 homair (insulin resistance index based on homa): 0.208918866,log10 homais (insulin secretion index based on homa): 1.791724058,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.606392115,insgenin (insulinogenic index): 1.811575006,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.552923608,log10 matsuda insulin sensitivity index: 0.697180682,muscle mass (%): 46.2,lg10 serum c-reactive protein (mg/l): 0.081347308,lg10 plasma adiponectin (mg/l): 0.591064607,ogtt fasting plasma free fatty acid (mmol/l): 0.22,ogtt 30 min plasma free fatty acid (mmol/l): 0.13,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9.6,ogtt 120 min plasma glucose (mmol/l): 7.2,log10 il1 receptor antagonist (pg/ml): 2.08817154,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.812913357,ogtt 30 min plasma insulin (mu/l): 1.696356389,ogtt 120 min plasma insulin (mu/l): 1.909556029,log10 ogtt fasting plasma proinsulin (pm/l): 1.117271296,ogtt 30 min plasma proinsulin (pm/l): 1.31386722,ogtt 120 min plasma proinsulin (pm/l): 1.766412847,log10 bioimpedance: Resistance: 2.660865478,log10 bioimpedance (reactance): 1.740362689,waist to hip ratio: 1.054347826,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.7930916,log10 ldl cholesterol (mmol/l): 0.624282096,log10 hdl cholesterol (mmol/l): 0.025305865,log10 total triglycerides (mmol/l): 0.23299611,log10 serum apoa1 (g/l): 0.041392685,log10 serum apob (g/l): 0.068185862,log10 urinary albumin excretion rate (ug/min): 0.726998728 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098311 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249210,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978138 | GSM1098311 | GSE45159 | 0.40019 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5273 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249210 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978138 |
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1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.441288134,log10 basal metabolic rate (kcal): 1557,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.405357412,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.716381171,plasma free fatty acids under the curve ogtt (mmol/l * min): 25.95,fat mass (%): 22.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.828136484,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 237,log10 homair (insulin resistance index based on homa): 0.545224622,log10 homais (insulin secretion index based on homa): 2.128029814,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.736930078,insgenin (insulinogenic index): 2.179551791,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.647529666,log10 matsuda insulin sensitivity index: 0.488595229,muscle mass (%): 41.2,lg10 serum c-reactive protein (mg/l): 0.2509077,lg10 plasma adiponectin (mg/l): 0.62324929,ogtt fasting plasma free fatty acid (mmol/l): 0.53,ogtt 30 min plasma free fatty acid (mmol/l): 0.27,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 6.2,log10 il1 receptor antagonist (pg/ml): 2.371990911,log10 il1 beta (pg/ml): -0.769551079,log10 ogtt fasting plasma insulin (mu/l): 1.149219113,ogtt 30 min plasma insulin (mu/l): 2.009875634,ogtt 120 min plasma insulin (mu/l): 1.785329835,log10 ogtt fasting plasma proinsulin (pm/l): 1.243038049,ogtt 30 min plasma proinsulin (pm/l): 1.6599162,ogtt 120 min plasma proinsulin (pm/l): 1.776701184,log10 bioimpedance: Resistance: 2.677606953,log10 bioimpedance (reactance): 1.591064607,waist to hip ratio: 1.005154639,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.62324929,log10 creatinine (umol/l): 1.929418926,log10 total cholesterol (mmol/l): 0.653212514,log10 ldl cholesterol (mmol/l): 0.457881897,log10 hdl cholesterol (mmol/l): 0.056904851,log10 total triglycerides (mmol/l): -0.070581074,log10 serum apoa1 (g/l): -0.022276395,log10 serum apob (g/l): -0.180456064,log10 urinary albumin excretion rate (ug/min): 0.831734078 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098312 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249211,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978139 | GSM1098312 | GSE45159 | 0.110692 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5352 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249211 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978139 |
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1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.468700338,log10 basal metabolic rate (kcal): 1658,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.027063902,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.509142232,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.7,fat mass (%): 26,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.439830884,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 94.5,log10 homair (insulin resistance index based on homa): 0.204119983,log10 homais (insulin secretion index based on homa): 1.982271233,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.495821753,insgenin (insulinogenic index): 2.243038049,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.417239121,log10 matsuda insulin sensitivity index: 0.833009944,muscle mass (%): 41.2,lg10 serum c-reactive protein (mg/l): 0.065206128,lg10 plasma adiponectin (mg/l): 0.799340549,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5,ogtt 30 min plasma glucose (mmol/l): 6.8,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.303865349,log10 il1 beta (pg/ml): -0.420216403,log10 ogtt fasting plasma insulin (mu/l): 0.857332496,ogtt 30 min plasma insulin (mu/l): 1.775974331,ogtt 120 min plasma insulin (mu/l): 1.531478917,log10 ogtt fasting plasma proinsulin (pm/l): 0.939519253,ogtt 30 min plasma proinsulin (pm/l): 1.385606274,ogtt 120 min plasma proinsulin (pm/l): 1.64738297,log10 bioimpedance: Resistance: 2.710963119,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 1.077669903,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.707570176,log10 creatinine (umol/l): 2.029383778,log10 total cholesterol (mmol/l): 0.802089258,log10 ldl cholesterol (mmol/l): 0.575187845,log10 hdl cholesterol (mmol/l): 0.271841607,log10 total triglycerides (mmol/l): 0.214843848,log10 serum apoa1 (g/l): 0.243038049,log10 serum apob (g/l): 0.08278537,log10 urinary albumin excretion rate (ug/min): 1.165804685 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098313 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249212,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978140 | GSM1098313 | GSE45159 | 0.254298 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5381 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249212 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978140 |
|
1 | age: 62,tissue: adipose tissue,log10 body mass index: 1.421150647,log10 basal metabolic rate (kcal): 1523,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.649133951,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.792506468,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.1,fat mass (%): 27.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.782179194,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 100.5,log10 homair (insulin resistance index based on homa): 0.113943352,log10 homais (insulin secretion index based on homa): 1.477121255,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.542065681,insgenin (insulinogenic index): 2.166510845,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.499673339,log10 matsuda insulin sensitivity index: 0.801906972,muscle mass (%): 34.2,lg10 serum c-reactive protein (mg/l): -0.552841969,lg10 plasma adiponectin (mg/l): 0.838849091,ogtt fasting plasma free fatty acid (mmol/l): 0.32,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6.5,ogtt 30 min plasma glucose (mmol/l): 8.7,ogtt 120 min plasma glucose (mmol/l): 5.8,log10 il1 receptor antagonist (pg/ml): 1.963126441,log10 il1 beta (pg/ml): -1,log10 ogtt fasting plasma insulin (mu/l): 0.653212514,ogtt 30 min plasma insulin (mu/l): 1.765668555,ogtt 120 min plasma insulin (mu/l): 1.697229343,log10 ogtt fasting plasma proinsulin (pm/l): 1.227886705,ogtt 30 min plasma proinsulin (pm/l): 1.720159303,ogtt 120 min plasma proinsulin (pm/l): 1.943494516,log10 bioimpedance: Resistance: 2.653212514,log10 bioimpedance (reactance): 1.544068044,waist to hip ratio: 0.923809524,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.804139432,log10 ldl cholesterol (mmol/l): 0.652246341,log10 hdl cholesterol (mmol/l): 0.193124598,log10 total triglycerides (mmol/l): 0.068185862,log10 serum apoa1 (g/l): 0.146128036,log10 serum apob (g/l): 0.079181246,log10 urinary albumin excretion rate (ug/min): 0.895989647 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098314 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249213,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978141 | GSM1098314 | GSE45159 | 0.001459 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5441 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249213 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978141 |
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1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.304401593,log10 basal metabolic rate (kcal): 1574,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.521311649,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.425976305,plasma free fatty acids under the curve ogtt (mmol/l * min): 3.15,fat mass (%): 14.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.108524457,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): -120,log10 homair (insulin resistance index based on homa): -0.0019345,log10 homais (insulin secretion index based on homa): 1.580870692,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.216693599,insgenin (insulinogenic index): 3.339252634,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.133219457,log10 matsuda insulin sensitivity index: 1.121763326,muscle mass (%): 48.1,lg10 serum c-reactive protein (mg/l): -0.21395879,lg10 plasma adiponectin (mg/l): 0.72427587,ogtt fasting plasma free fatty acid (mmol/l): 0.07,ogtt 30 min plasma free fatty acid (mmol/l): 0.02,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 5.7,ogtt 120 min plasma glucose (mmol/l): 2.8,log10 il1 receptor antagonist (pg/ml): 1.950413539,log10 il1 beta (pg/ml): -0.721246399,log10 ogtt fasting plasma insulin (mu/l): 0.602059991,ogtt 30 min plasma insulin (mu/l): 1.606381365,ogtt 120 min plasma insulin (mu/l): 0.763427994,log10 ogtt fasting plasma proinsulin (pm/l): 0.707570176,ogtt 30 min plasma proinsulin (pm/l): 1.012837225,ogtt 120 min plasma proinsulin (pm/l): 0.939519253,log10 bioimpedance: Resistance: 2.757396029,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 0.931578947,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.146128036,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.754348336,log10 ldl cholesterol (mmol/l): 0.523746467,log10 hdl cholesterol (mmol/l): 0.187520721,log10 total triglycerides (mmol/l): -0.142667504,log10 serum apoa1 (g/l): 0.136720567,log10 serum apob (g/l): -0.036212173,log10 urinary albumin excretion rate (ug/min): 1.286065129 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098315 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249214,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978142 | GSM1098315 | GSE45159 | 0.367341 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5446 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249214 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978142 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.330812301,log10 basal metabolic rate (kcal): 1601,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.56346251,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.362966508,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.95,fat mass (%): 10.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.395534135,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 97.5,log10 homair (insulin resistance index based on homa): -0.079876674,log10 homais (insulin secretion index based on homa): 1.77815125,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.154819436,insgenin (insulinogenic index): 1.988611411,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.059752694,log10 matsuda insulin sensitivity index: 1.157029579,muscle mass (%): 52.8,lg10 serum c-reactive protein (mg/l): 0.019531685,lg10 plasma adiponectin (mg/l): 0.963787827,ogtt fasting plasma free fatty acid (mmol/l): 0.21,ogtt 30 min plasma free fatty acid (mmol/l): 0.1,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 4.8,ogtt 30 min plasma glucose (mmol/l): 6.5,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 1.932930143,log10 il1 beta (pg/ml): -0.443697499,log10 ogtt fasting plasma insulin (mu/l): 0.591064607,ogtt 30 min plasma insulin (mu/l): 1.498310554,ogtt 120 min plasma insulin (mu/l): 0.982271233,log10 ogtt fasting plasma proinsulin (pm/l): 1.008600172,ogtt 30 min plasma proinsulin (pm/l): 1.378397901,ogtt 120 min plasma proinsulin (pm/l): 1.372912003,log10 bioimpedance: Resistance: 2.666517981,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 0.843243243,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.788875116,log10 ldl cholesterol (mmol/l): 0.471291711,log10 hdl cholesterol (mmol/l): 0.354108439,log10 total triglycerides (mmol/l): 0.06069784,log10 serum apoa1 (g/l): 0.290034611,log10 serum apob (g/l): -0.036212173,log10 urinary albumin excretion rate (ug/min): 1.213585283 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098316 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249215,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978143 | GSM1098316 | GSE45159 | 0.026548 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5458 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249215 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978143 |
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1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.524472085,log10 basal metabolic rate (kcal): 1657,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.296721789,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.896289059,plasma free fatty acids under the curve ogtt (mmol/l * min): 36.6,fat mass (%): 28.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.73470962,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 228,log10 homair (insulin resistance index based on homa): 0.706243506,log10 homais (insulin secretion index based on homa): 2.413003755,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.836425397,insgenin (insulinogenic index): 2.314643241,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.722436471,log10 matsuda insulin sensitivity index: 0.379606257,muscle mass (%): 39.4,lg10 serum c-reactive protein (mg/l): 0.705692697,lg10 plasma adiponectin (mg/l): 0.973127854,ogtt fasting plasma free fatty acid (mmol/l): 0.53,ogtt 30 min plasma free fatty acid (mmol/l): 0.44,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 5.2,log10 il1 receptor antagonist (pg/ml): 2.542339841,log10 il1 beta (pg/ml): -0.795880017,log10 ogtt fasting plasma insulin (mu/l): 1.342422681,ogtt 30 min plasma insulin (mu/l): 2.183839037,ogtt 120 min plasma insulin (mu/l): 1.635483747,log10 ogtt fasting plasma proinsulin (pm/l): 1.274157849,ogtt 30 min plasma proinsulin (pm/l): 1.607455023,ogtt 120 min plasma proinsulin (pm/l): 1.810904281,log10 bioimpedance: Resistance: 2.669316881,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 1.09009009,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.754348336,log10 ldl cholesterol (mmol/l): 0.582063363,log10 hdl cholesterol (mmol/l): 0.06069784,log10 total triglycerides (mmol/l): 0.079181246,log10 serum apoa1 (g/l): 0.093421685,log10 serum apob (g/l): 0.064457989,log10 urinary albumin excretion rate (ug/min): 1.068523178 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098317 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249216,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978144 | GSM1098317 | GSE45159 | 0.425425 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5470 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249216 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978144 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.518901503,log10 basal metabolic rate (kcal): 1581,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.454927697,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.922418135,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.2,fat mass (%): 27.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.12023788,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 453,log10 homair (insulin resistance index based on homa): 0.29666519,log10 homais (insulin secretion index based on homa): 1.908485019,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.694052108,insgenin (insulinogenic index): 1.782698878,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.639536291,log10 matsuda insulin sensitivity index: 0.576841583,muscle mass (%): 40.1,lg10 serum c-reactive protein (mg/l): -0.18243463,lg10 plasma adiponectin (mg/l): 0.819543936,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.27,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 10.5,log10 il1 receptor antagonist (pg/ml): 2.08174325,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.908485019,ogtt 30 min plasma insulin (mu/l): 1.667452953,ogtt 120 min plasma insulin (mu/l): 2.073351702,log10 ogtt fasting plasma proinsulin (pm/l): 1.269512944,ogtt 30 min plasma proinsulin (pm/l): 1.57054294,ogtt 120 min plasma proinsulin (pm/l): 1.892094603,log10 bioimpedance: Resistance: 2.673020907,log10 bioimpedance (reactance): 1.69019608,waist to hip ratio: 1.004424779,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.462397998,log10 creatinine (umol/l): 1.919078092,log10 total cholesterol (mmol/l): 0.751279104,log10 ldl cholesterol (mmol/l): 0.59439255,log10 hdl cholesterol (mmol/l): 0.139879086,log10 total triglycerides (mmol/l): 0.056904851,log10 serum apoa1 (g/l): 0.120573931,log10 serum apob (g/l): 0.025305865,log10 urinary albumin excretion rate (ug/min): 0.965004339 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098318 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249217,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978145 | GSM1098318 | GSE45159 | 0.268179 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5510 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249217 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978145 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.390819468,log10 basal metabolic rate (kcal): 1383,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.406090767,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.370626497,plasma free fatty acids under the curve ogtt (mmol/l * min): 26.1,fat mass (%): 17.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.77478706,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 204,log10 homair (insulin resistance index based on homa): 0.456703349,log10 homais (insulin secretion index based on homa): 2.039508541,log10 insulin area under the curve (ogtt) (pmol/l * min): 5.051465102,insgenin (insulinogenic index): 2.666218364,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 5.018288472,log10 matsuda insulin sensitivity index: 0.385560038,muscle mass (%): 44.3,lg10 serum c-reactive protein (mg/l): 0.373647472,lg10 plasma adiponectin (mg/l): 0.633468456,ogtt fasting plasma free fatty acid (mmol/l): 0.36,ogtt 30 min plasma free fatty acid (mmol/l): 0.27,ogtt 120 min plasma free fatty acid (mmol/l): 0.1,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.1,ogtt 120 min plasma glucose (mmol/l): 6.8,log10 il1 receptor antagonist (pg/ml): 2.263754389,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.06069784,ogtt 30 min plasma insulin (mu/l): 2.311117843,ogtt 120 min plasma insulin (mu/l): 2.146748014,log10 ogtt fasting plasma proinsulin (pm/l): 1.305351369,ogtt 30 min plasma proinsulin (pm/l): 1.804820679,ogtt 120 min plasma proinsulin (pm/l): 1.984527313,log10 bioimpedance: Resistance: 2.705863712,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.936842105,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.531478917,log10 creatinine (umol/l): 1.934498451,log10 total cholesterol (mmol/l): 0.710117365,log10 ldl cholesterol (mmol/l): 0.558708571,log10 hdl cholesterol (mmol/l): -0.013228266,log10 total triglycerides (mmol/l): 0.250420002,log10 serum apoa1 (g/l): 0.068185862,log10 serum apob (g/l): 0.049218023,log10 urinary albumin excretion rate (ug/min): 0.556302501 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098319 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249218,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978146 | GSM1098319 | GSE45159 | 0.079484 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5521 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249218 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978146 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.344976306,log10 basal metabolic rate (kcal): 1504,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.507089067,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.464018176,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.75,fat mass (%): 15.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.46454575,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 106.5,log10 homair (insulin resistance index based on homa): -0.096910013,log10 homais (insulin secretion index based on homa): 1.681241237,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.212879792,insgenin (insulinogenic index): 1.948412966,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.137797043,log10 matsuda insulin sensitivity index: 1.125689382,muscle mass (%): 47.6,lg10 serum c-reactive protein (mg/l): -0.222573178,lg10 plasma adiponectin (mg/l): 0.806179974,ogtt fasting plasma free fatty acid (mmol/l): 0.29,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5,ogtt 30 min plasma glucose (mmol/l): 7,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.05709529,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.556302501,ogtt 30 min plasma insulin (mu/l): 1.521138084,ogtt 120 min plasma insulin (mu/l): 1.176091259,log10 ogtt fasting plasma proinsulin (pm/l): 1.012837225,ogtt 30 min plasma proinsulin (pm/l): 1.394451681,ogtt 120 min plasma proinsulin (pm/l): 1.506505032,log10 bioimpedance: Resistance: 2.720159303,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 0.90625,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.62324929,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.712649702,log10 ldl cholesterol (mmol/l): 0.567026366,log10 hdl cholesterol (mmol/l): 0.133538908,log10 total triglycerides (mmol/l): 0.071882007,log10 serum apoa1 (g/l): 0.1430148,log10 serum apob (g/l): 0.029383778,log10 urinary albumin excretion rate (ug/min): 0.878266403 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098320 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249219,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978147 | GSM1098320 | GSE45159 | 0.475497 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5530 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249219 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978147 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.544837789,log10 basal metabolic rate (kcal): 1744,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.352532716,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.083358352,plasma free fatty acids under the curve ogtt (mmol/l * min): 27.75,fat mass (%): 28.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.842350343,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 174,log10 homair (insulin resistance index based on homa): 0.337836263,log10 homais (insulin secretion index based on homa): 1.767293323,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.286276786,insgenin (insulinogenic index): 1.709886419,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.134941711,log10 matsuda insulin sensitivity index: 0.82058713,muscle mass (%): 38.9,lg10 serum c-reactive protein (mg/l): 0.581835924,lg10 plasma adiponectin (mg/l): 0.832508913,ogtt fasting plasma free fatty acid (mmol/l): 0.54,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 6.2,ogtt 30 min plasma glucose (mmol/l): 10.6,ogtt 120 min plasma glucose (mmol/l): 4.2,log10 il1 receptor antagonist (pg/ml): 2.527436552,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.897627091,ogtt 30 min plasma insulin (mu/l): 1.658011397,ogtt 120 min plasma insulin (mu/l): 0.919078092,log10 ogtt fasting plasma proinsulin (pm/l): 1.206825876,ogtt 30 min plasma proinsulin (pm/l): 1.492760389,ogtt 120 min plasma proinsulin (pm/l): 1.547774705,log10 bioimpedance: Resistance: 2.62838893,log10 bioimpedance (reactance): 1.591064607,waist to hip ratio: 1.049586777,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.462397998,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.812913357,log10 ldl cholesterol (mmol/l): 0.644438589,log10 hdl cholesterol (mmol/l): 0.152288344,log10 total triglycerides (mmol/l): 0.079181246,log10 serum apoa1 (g/l): 0.146128036,log10 serum apob (g/l): 0.1430148,log10 urinary albumin excretion rate (ug/min): 0.719398939 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098321 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249220,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978148 | GSM1098321 | GSE45159 | 0.160567 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5538 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249220 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978148 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.335891783,log10 basal metabolic rate (kcal): 1402,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.527231569,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.291476642,plasma free fatty acids under the curve ogtt (mmol/l * min): 24.9,fat mass (%): 11.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.856425529,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 219,log10 homair (insulin resistance index based on homa): 0.108865574,log10 homais (insulin secretion index based on homa): 1.611014834,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.228400359,insgenin (insulinogenic index): 1.436327184,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.126845441,log10 matsuda insulin sensitivity index: 0.935384417,muscle mass (%): 47.1,lg10 serum c-reactive protein (mg/l): -0.145693958,lg10 plasma adiponectin (mg/l): 0.995635195,ogtt fasting plasma free fatty acid (mmol/l): 0.45,ogtt 30 min plasma free fatty acid (mmol/l): 0.25,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 8.8,ogtt 120 min plasma glucose (mmol/l): 6.9,log10 il1 receptor antagonist (pg/ml): 2.300443302,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.69019608,ogtt 30 min plasma insulin (mu/l): 1.257678575,ogtt 120 min plasma insulin (mu/l): 1.567026366,log10 ogtt fasting plasma proinsulin (pm/l): 0.763427994,ogtt 30 min plasma proinsulin (pm/l): 0.908485019,ogtt 120 min plasma proinsulin (pm/l): 1.383815366,log10 bioimpedance: Resistance: 2.681241237,log10 bioimpedance (reactance): 1.602059991,waist to hip ratio: 0.887755102,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.230448921,log10 creatinine (umol/l): 1.897627091,log10 total cholesterol (mmol/l): 0.679427897,log10 ldl cholesterol (mmol/l): 0.51851394,log10 hdl cholesterol (mmol/l): 0.10720997,log10 total triglycerides (mmol/l): 0.037426498,log10 serum apoa1 (g/l): 0.079181246,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 0.750713002 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098322 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249221,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978149 | GSM1098322 | GSE45159 | 0.196946 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5571 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249221 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978149 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.448010631,log10 basal metabolic rate (kcal): 1838,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.352532716,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.753896583,plasma free fatty acids under the curve ogtt (mmol/l * min): 24.15,fat mass (%): 19.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.811374694,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 238.5,log10 homair (insulin resistance index based on homa): 0.546542663,log10 homais (insulin secretion index based on homa): 2.158362492,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.826223863,insgenin (insulinogenic index): 2.16501338,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.753238244,log10 matsuda insulin sensitivity index: 0.430513043,muscle mass (%): 45.7,lg10 serum c-reactive protein (mg/l): 0.079904468,lg10 plasma adiponectin (mg/l): 0.556302501,ogtt fasting plasma free fatty acid (mmol/l): 0.3,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 8.2,ogtt 120 min plasma glucose (mmol/l): 7.2,log10 il1 receptor antagonist (pg/ml): 2.161278139,log10 il1 beta (pg/ml): -0.356547324,log10 ogtt fasting plasma insulin (mu/l): 1.158362492,ogtt 30 min plasma insulin (mu/l): 1.904174368,ogtt 120 min plasma insulin (mu/l): 2.135132651,log10 ogtt fasting plasma proinsulin (pm/l): 1.086359831,ogtt 30 min plasma proinsulin (pm/l): 1.350248018,ogtt 120 min plasma proinsulin (pm/l): 1.770852012,log10 bioimpedance: Resistance: 2.598790507,log10 bioimpedance (reactance): 1.602059991,waist to hip ratio: 0.971153846,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.462397998,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.707570176,log10 ldl cholesterol (mmol/l): 0.53529412,log10 hdl cholesterol (mmol/l): -0.036212173,log10 total triglycerides (mmol/l): 0.374748346,log10 serum apoa1 (g/l): 0.071882007,log10 serum apob (g/l): 0.123851641,log10 urinary albumin excretion rate (ug/min): 0.993174596 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098323 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249222,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978150 | GSM1098323 | GSE45159 | 0.29008 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5606 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249222 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978150 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.364399523,log10 basal metabolic rate (kcal): 1759,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 5.996232093,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.143839455,plasma free fatty acids under the curve ogtt (mmol/l * min): 7.5,fat mass (%): 16.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.703903573,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 90,log10 homair (insulin resistance index based on homa): 0.180571861,log10 homais (insulin secretion index based on homa): 1.610028921,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.378797486,insgenin (insulinogenic index): 2.341434525,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.300204051,log10 matsuda insulin sensitivity index: 0.862961273,muscle mass (%): 49.2,lg10 serum c-reactive protein (mg/l): -0.853871964,lg10 plasma adiponectin (mg/l): 0.73239376,ogtt fasting plasma free fatty acid (mmol/l): 0.12,ogtt 30 min plasma free fatty acid (mmol/l): 0.08,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6.2,ogtt 30 min plasma glucose (mmol/l): 7.4,ogtt 120 min plasma glucose (mmol/l): 6.6,log10 il1 receptor antagonist (pg/ml): 2.149496233,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.740362689,ogtt 30 min plasma insulin (mu/l): 1.693726949,ogtt 120 min plasma insulin (mu/l): 1.320146286,log10 ogtt fasting plasma proinsulin (pm/l): 1.29666519,ogtt 30 min plasma proinsulin (pm/l): 1.615950052,ogtt 120 min plasma proinsulin (pm/l): 1.742725131,log10 bioimpedance: Resistance: 2.689308859,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 0.936170213,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.531478917,log10 creatinine (umol/l): 2.037426498,log10 total cholesterol (mmol/l): 0.58546073,log10 ldl cholesterol (mmol/l): 0.303196057,log10 hdl cholesterol (mmol/l): 0.10720997,log10 total triglycerides (mmol/l): 0.113943352,log10 serum apoa1 (g/l): 0.071882007,log10 serum apob (g/l): -0.15490196,log10 urinary albumin excretion rate (ug/min): 0.576505887 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098324 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249223,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978151 | GSM1098324 | GSE45159 | 0.111241 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5680 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249223 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978151 |
|
1 | age: 61,tissue: adipose tissue,log10 body mass index: 1.405392229,log10 basal metabolic rate (kcal): 1631,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.096974819,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.194191319,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.5,fat mass (%): 25.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.825753833,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 259.5,log10 homair (insulin resistance index based on homa): 0.324693914,log10 homais (insulin secretion index based on homa): 1.966759067,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.418135498,insgenin (insulinogenic index): 1.723530299,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.297848018,log10 matsuda insulin sensitivity index: 0.757773977,muscle mass (%): 48.8,lg10 serum c-reactive protein (mg/l): 0.124830149,lg10 plasma adiponectin (mg/l): 0.431363764,ogtt fasting plasma free fatty acid (mmol/l): 0.18,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.12,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 9.8,ogtt 120 min plasma glucose (mmol/l): 5.3,log10 il1 receptor antagonist (pg/ml): 2.633952979,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.944482672,ogtt 30 min plasma insulin (mu/l): 1.677606953,ogtt 120 min plasma insulin (mu/l): 1.485721426,log10 ogtt fasting plasma proinsulin (pm/l): 0.72427587,ogtt 30 min plasma proinsulin (pm/l): 1.056904851,ogtt 120 min plasma proinsulin (pm/l): 1.374748346,log10 bioimpedance: Resistance: 2.658011397,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.927083333,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.477121255,log10 creatinine (umol/l): 2.008600172,log10 total cholesterol (mmol/l): 0.846955325,log10 ldl cholesterol (mmol/l): 0.662757832,log10 hdl cholesterol (mmol/l): 0.149219113,log10 total triglycerides (mmol/l): 0.281033367,log10 serum apoa1 (g/l): 0.1430148,log10 serum apob (g/l): 0.158362492,log10 urinary albumin excretion rate (ug/min): 0.84509804 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098325 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249224,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978152 | GSM1098325 | GSE45159 | 0.182899 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5708 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249224 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978152 |
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1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.42199149,log10 basal metabolic rate (kcal): 1667,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.405357412,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.530514625,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.45,fat mass (%): 17.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.832890014,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 144,log10 homair (insulin resistance index based on homa): 0.10720997,log10 homais (insulin secretion index based on homa): 1.491844512,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.329906123,insgenin (insulinogenic index): 1.882239848,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.25851756,log10 matsuda insulin sensitivity index: 0.900831072,muscle mass (%): 47.4,lg10 serum c-reactive protein (mg/l): -0.28567024,lg10 plasma adiponectin (mg/l): 0.755874856,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.15,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 8.8,ogtt 120 min plasma glucose (mmol/l): 6.4,log10 il1 receptor antagonist (pg/ml): 2.119486836,log10 il1 beta (pg/ml): -1,log10 ogtt fasting plasma insulin (mu/l): 0.653212514,ogtt 30 min plasma insulin (mu/l): 1.544068044,ogtt 120 min plasma insulin (mu/l): 1.491361694,log10 ogtt fasting plasma proinsulin (pm/l): 1,ogtt 30 min plasma proinsulin (pm/l): 1.227886705,ogtt 120 min plasma proinsulin (pm/l): 1.447158031,log10 bioimpedance: Resistance: 2.631443769,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 1.01,log10 serum bilirubin (umol/l): 1.204119983,log10 serum alanine aminotransfrase (u/l): 1.568201724,log10 creatinine (umol/l): 1.929418926,log10 total cholesterol (mmol/l): 0.758911892,log10 ldl cholesterol (mmol/l): 0.606381365,log10 hdl cholesterol (mmol/l): 0.08278537,log10 total triglycerides (mmol/l): -0.086186148,log10 serum apoa1 (g/l): 0.053078443,log10 serum apob (g/l): 0.017033339,log10 urinary albumin excretion rate (ug/min): 0.994009636 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098326 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249225,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978153 | GSM1098326 | GSE45159 | 0.208255 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5812 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249225 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978153 |
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1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.435831373,log10 basal metabolic rate (kcal): 1778,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.283532704,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.530918856,plasma free fatty acids under the curve ogtt (mmol/l * min): 21.3,fat mass (%): 16.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.893301531,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 255,log10 homair (insulin resistance index based on homa): -0.008970928,log10 homais (insulin secretion index based on homa): 1.519085756,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.413182371,insgenin (insulinogenic index): 1.884698681,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.364682296,log10 matsuda insulin sensitivity index: 0.931283927,muscle mass (%): 48.7,lg10 serum c-reactive protein (mg/l): 0.005609445,lg10 plasma adiponectin (mg/l): 0.819543936,ogtt fasting plasma free fatty acid (mmol/l): 0.41,ogtt 30 min plasma free fatty acid (mmol/l): 0.23,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 9.9,ogtt 120 min plasma glucose (mmol/l): 6,log10 il1 receptor antagonist (pg/ml): 2.44557307,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.579783597,ogtt 30 min plasma insulin (mu/l): 1.749736316,ogtt 120 min plasma insulin (mu/l): 1.294466226,log10 ogtt fasting plasma proinsulin (pm/l): 1,ogtt 30 min plasma proinsulin (pm/l): 1.511883361,ogtt 120 min plasma proinsulin (pm/l): 1.695481676,log10 bioimpedance: Resistance: 2.56937391,log10 bioimpedance (reactance): 1.602059991,waist to hip ratio: 0.945,log10 serum bilirubin (umol/l): 1.447158031,log10 serum alanine aminotransfrase (u/l): 1.113943352,log10 creatinine (umol/l): 1.963787827,log10 total cholesterol (mmol/l): 0.796574333,log10 ldl cholesterol (mmol/l): 0.613841822,log10 hdl cholesterol (mmol/l): 0.195899652,log10 total triglycerides (mmol/l): 0.243038049,log10 serum apoa1 (g/l): 0.220108088,log10 serum apob (g/l): 0.139879086,log10 urinary albumin excretion rate (ug/min): 0.484946592 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098327 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249226,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978154 | GSM1098327 | GSE45159 | 0.106747 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5845 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249226 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978154 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.497613484,log10 basal metabolic rate (kcal): 1697,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.385885025,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.723094172,plasma free fatty acids under the curve ogtt (mmol/l * min): 30,fat mass (%): 20.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.1376316,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 358.5,log10 homair (insulin resistance index based on homa): 0.491423954,log10 homais (insulin secretion index based on homa): 1.876058496,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.661897833,insgenin (insulinogenic index): 1.972863765,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.580480195,log10 matsuda insulin sensitivity index: 0.496833332,muscle mass (%): 45,lg10 serum c-reactive protein (mg/l): 0.008174184,lg10 plasma adiponectin (mg/l): 0.612783857,ogtt fasting plasma free fatty acid (mmol/l): 0.4,ogtt 30 min plasma free fatty acid (mmol/l): 0.34,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 9.9,ogtt 120 min plasma glucose (mmol/l): 9.7,log10 il1 receptor antagonist (pg/ml): 2.615297594,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.037426498,ogtt 30 min plasma insulin (mu/l): 1.81756537,ogtt 120 min plasma insulin (mu/l): 1.896526217,log10 ogtt fasting plasma proinsulin (pm/l): 1.285557309,ogtt 30 min plasma proinsulin (pm/l): 1.649334859,ogtt 120 min plasma proinsulin (pm/l): 1.959041392,log10 bioimpedance: Resistance: 2.553883027,log10 bioimpedance (reactance): 1.568201724,waist to hip ratio: 1.058252427,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.857332496,log10 creatinine (umol/l): 1.934498451,log10 total cholesterol (mmol/l): 0.673020907,log10 ldl cholesterol (mmol/l): 0.445604203,log10 hdl cholesterol (mmol/l): 0.06069784,log10 total triglycerides (mmol/l): 0.178976947,log10 serum apoa1 (g/l): 0.133538908,log10 serum apob (g/l): -0.013228266,log10 urinary albumin excretion rate (ug/min): 0.988520182 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098328 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249227,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978155 | GSM1098328 | GSE45159 | 0.138671 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5859 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249227 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978155 |
|
1 | age: 66,tissue: adipose tissue,log10 body mass index: 1.395786131,log10 basal metabolic rate (kcal): 1337,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.319697249,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.101353554,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.65,fat mass (%): 30.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.835260919,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 265.5,log10 homair (insulin resistance index based on homa): 0.401400541,log10 homais (insulin secretion index based on homa): 2.043465694,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.795977288,insgenin (insulinogenic index): 2.253257214,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.739999309,log10 matsuda insulin sensitivity index: 0.53533941,muscle mass (%): 44.2,lg10 serum c-reactive protein (mg/l): -0.369572125,lg10 plasma adiponectin (mg/l): 0.86923172,ogtt fasting plasma free fatty acid (mmol/l): 0.53,ogtt 30 min plasma free fatty acid (mmol/l): 0.23,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 6.5,log10 il1 receptor antagonist (pg/ml): 2.473457773,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.021189299,ogtt 30 min plasma insulin (mu/l): 2.071882007,ogtt 120 min plasma insulin (mu/l): 1.849419414,log10 ogtt fasting plasma proinsulin (pm/l): 1.120573931,ogtt 30 min plasma proinsulin (pm/l): 1.655138435,ogtt 120 min plasma proinsulin (pm/l): 1.806179974,log10 bioimpedance: Resistance: 2.726727209,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 0.969072165,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.380211242,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.662757832,log10 ldl cholesterol (mmol/l): 0.404833717,log10 hdl cholesterol (mmol/l): 0.23299611,log10 total triglycerides (mmol/l): -0.187086643,log10 serum apoa1 (g/l): 0.164352856,log10 serum apob (g/l): -0.091514981,log10 urinary albumin excretion rate (ug/min): 0.841007324 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098329 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249228,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978156 | GSM1098329 | GSE45159 | 0.06056 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5877 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249228 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978156 |
|
1 | age: 64,tissue: adipose tissue,log10 body mass index: 1.407645014,log10 basal metabolic rate (kcal): 1488,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.132615804,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.254470268,plasma free fatty acids under the curve ogtt (mmol/l * min): 24.3,fat mass (%): 30.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.77478706,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 168,log10 homair (insulin resistance index based on homa): -0.013128782,log10 homais (insulin secretion index based on homa): 1.489020478,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.291302236,insgenin (insulinogenic index): 1.912965621,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.227706782,log10 matsuda insulin sensitivity index: 0.998144248,muscle mass (%): 33.9,lg10 serum c-reactive protein (mg/l): 0.033021445,lg10 plasma adiponectin (mg/l): 0.86923172,ogtt fasting plasma free fatty acid (mmol/l): 0.29,ogtt 30 min plasma free fatty acid (mmol/l): 0.31,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 8.4,ogtt 120 min plasma glucose (mmol/l): 6.3,log10 il1 receptor antagonist (pg/ml): 2.292765404,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.568201724,ogtt 30 min plasma insulin (mu/l): 1.5774918,ogtt 120 min plasma insulin (mu/l): 1.318063335,log10 ogtt fasting plasma proinsulin (pm/l): 1,ogtt 30 min plasma proinsulin (pm/l): 1.281033367,ogtt 120 min plasma proinsulin (pm/l): 1.547774705,log10 bioimpedance: Resistance: 2.705863712,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 0.951456311,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.146128036,log10 creatinine (umol/l): 1.995635195,log10 total cholesterol (mmol/l): 0.657055853,log10 ldl cholesterol (mmol/l): 0.505149978,log10 hdl cholesterol (mmol/l): -0.080921908,log10 total triglycerides (mmol/l): 0.167317335,log10 serum apoa1 (g/l): -0.008773924,log10 serum apob (g/l): 0.025305865,log10 urinary albumin excretion rate (ug/min): 0.584447206 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098330 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249229,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978157 | GSM1098330 | GSE45159 | 0.167101 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5901 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249229 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978157 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.419141302,log10 basal metabolic rate (kcal): 1663,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.322656165,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.640784241,plasma free fatty acids under the curve ogtt (mmol/l * min): 25.05,fat mass (%): 21.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.596189756,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 78,log10 homair (insulin resistance index based on homa): 0.143639235,log10 homais (insulin secretion index based on homa): 1.671695919,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.225154149,insgenin (insulinogenic index): 2.065608439,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.110791661,log10 matsuda insulin sensitivity index: 0.965479674,muscle mass (%): 44.4,lg10 serum c-reactive protein (mg/l): -0.223298816,lg10 plasma adiponectin (mg/l): 0.968482949,ogtt fasting plasma free fatty acid (mmol/l): 0.28,ogtt 30 min plasma free fatty acid (mmol/l): 0.31,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 7.1,ogtt 120 min plasma glucose (mmol/l): 5.8,log10 il1 receptor antagonist (pg/ml): 2.300312818,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.73239376,ogtt 30 min plasma insulin (mu/l): 1.485721426,ogtt 120 min plasma insulin (mu/l): 1.292256071,log10 ogtt fasting plasma proinsulin (pm/l): 1.08278537,ogtt 30 min plasma proinsulin (pm/l): 1.309630167,ogtt 120 min plasma proinsulin (pm/l): 1.557507202,log10 bioimpedance: Resistance: 2.704150517,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.970873786,log10 serum bilirubin (umol/l): 1.491361694,log10 serum alanine aminotransfrase (u/l): 1.380211242,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.632457292,log10 ldl cholesterol (mmol/l): 0.408239965,log10 hdl cholesterol (mmol/l): 0.214843848,log10 total triglycerides (mmol/l): -0.22184875,log10 serum apoa1 (g/l): 0.133538908,log10 serum apob (g/l): -0.142667504,log10 urinary albumin excretion rate (ug/min): 0.812704511 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098331 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249230,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978158 | GSM1098331 | GSE45159 | 0.050727 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5909 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249230 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978158 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.4015437,log10 basal metabolic rate (kcal): 1786,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.43621404,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.696627483,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.15,fat mass (%): 18.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.835260919,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 121.5,log10 homair (insulin resistance index based on homa): 0.157557497,log10 homais (insulin secretion index based on homa): 1.499864382,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.408782494,insgenin (insulinogenic index): 1.901881935,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.344470872,log10 matsuda insulin sensitivity index: 0.836066685,muscle mass (%): 47.9,lg10 serum c-reactive protein (mg/l): -0.016824928,lg10 plasma adiponectin (mg/l): 0.653212514,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.16,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6.6,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 5.7,log10 il1 receptor antagonist (pg/ml): 2.531951275,log10 il1 beta (pg/ml): -0.397940009,log10 ogtt fasting plasma insulin (mu/l): 0.69019608,ogtt 30 min plasma insulin (mu/l): 1.610660163,ogtt 120 min plasma insulin (mu/l): 1.589949601,log10 ogtt fasting plasma proinsulin (pm/l): 0.806179974,ogtt 30 min plasma proinsulin (pm/l): 1.195899652,ogtt 120 min plasma proinsulin (pm/l): 1.609594409,log10 bioimpedance: Resistance: 2.670245853,log10 bioimpedance (reactance): 1.740362689,waist to hip ratio: 0.941176471,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 1.929418926,log10 total cholesterol (mmol/l): 0.612783857,log10 ldl cholesterol (mmol/l): 0.408239965,log10 hdl cholesterol (mmol/l): 0.093421685,log10 total triglycerides (mmol/l): 0.004321374,log10 serum apoa1 (g/l): 0.079181246,log10 serum apob (g/l): -0.086186148,log10 urinary albumin excretion rate (ug/min): 1.273986699 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098332 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249231,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978159 | GSM1098332 | GSE45159 | 0.097183 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5935 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249231 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978159 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.389442446,log10 basal metabolic rate (kcal): 1714,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.320124728,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.536787711,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.2,fat mass (%): 20,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.476746204,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 64.5,log10 homair (insulin resistance index based on homa): -0.142667504,log10 homais (insulin secretion index based on homa): 1.499397649,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.158090973,insgenin (insulinogenic index): 1.973838066,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.087461966,log10 matsuda insulin sensitivity index: 1.160980214,muscle mass (%): 46.1,lg10 serum c-reactive protein (mg/l): -0.355561411,lg10 plasma adiponectin (mg/l): 1.045322979,ogtt fasting plasma free fatty acid (mmol/l): 0.3,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 6.7,ogtt 120 min plasma glucose (mmol/l): 5.1,log10 il1 receptor antagonist (pg/ml): 2.313888302,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.477121255,ogtt 30 min plasma insulin (mu/l): 1.369215857,ogtt 120 min plasma insulin (mu/l): 1.324282455,log10 ogtt fasting plasma proinsulin (pm/l): 1.025305865,ogtt 30 min plasma proinsulin (pm/l): 1.201397124,ogtt 120 min plasma proinsulin (pm/l): 1.399673721,log10 bioimpedance: Resistance: 2.710963119,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 0.886792453,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.544068044,log10 creatinine (umol/l): 1.954242509,log10 total cholesterol (mmol/l): 0.766412847,log10 ldl cholesterol (mmol/l): 0.597695186,log10 hdl cholesterol (mmol/l): 0.206825876,log10 total triglycerides (mmol/l): 0.017033339,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): 0.053078443,log10 urinary albumin excretion rate (ug/min): 0.757875294 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098333 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249232,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978160 | GSM1098333 | GSE45159 | 0.210525 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM5951 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249232 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978160 |
|
1 | age: 61,tissue: adipose tissue,log10 body mass index: 1.428877436,log10 basal metabolic rate (kcal): 1481,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.250764396,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.355292058,plasma free fatty acids under the curve ogtt (mmol/l * min): 13.65,fat mass (%): 30.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.518653156,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 49.5,log10 homair (insulin resistance index based on homa): 0.037160793,log10 homais (insulin secretion index based on homa): 1.59207577,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.28425021,insgenin (insulinogenic index): 1.991226076,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.208064948,log10 matsuda insulin sensitivity index: 1.026440046,muscle mass (%): 40.5,lg10 serum c-reactive protein (mg/l): -0.132532512,lg10 plasma adiponectin (mg/l): 1.10720997,ogtt fasting plasma free fatty acid (mmol/l): 0.42,ogtt 30 min plasma free fatty acid (mmol/l): 0.1,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 8.4,ogtt 120 min plasma glucose (mmol/l): 3.2,log10 il1 receptor antagonist (pg/ml): 2.620302659,log10 il1 beta (pg/ml): -0.200659451,log10 ogtt fasting plasma insulin (mu/l): 0.633468456,ogtt 30 min plasma insulin (mu/l): 1.684845362,ogtt 120 min plasma insulin (mu/l): 0.72427587,log10 ogtt fasting plasma proinsulin (pm/l): 0.748188027,ogtt 30 min plasma proinsulin (pm/l): 1.434568904,ogtt 120 min plasma proinsulin (pm/l): 1.31386722,log10 bioimpedance: Resistance: 2.685741739,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.931372549,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.707570176,log10 creatinine (umol/l): 1.968482949,log10 total cholesterol (mmol/l): 0.827369273,log10 ldl cholesterol (mmol/l): 0.656098202,log10 hdl cholesterol (mmol/l): 0.29666519,log10 total triglycerides (mmol/l): -0.124938737,log10 serum apoa1 (g/l): 0.247973266,log10 serum apob (g/l): 0.071882007,log10 urinary albumin excretion rate (ug/min): 0.713425921 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098334 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249233,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978161 | GSM1098334 | GSE45159 | 0.044194 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6006 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249233 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978161 |
|
1 | age: 66,tissue: adipose tissue,log10 body mass index: 1.398578074,log10 basal metabolic rate (kcal): 1461,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.700688735,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.595388241,plasma free fatty acids under the curve ogtt (mmol/l * min): 12.75,fat mass (%): 25,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.539158811,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 84,log10 homair (insulin resistance index based on homa): 0.021648627,log10 homais (insulin secretion index based on homa): 1.633468456,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.456533037,insgenin (insulinogenic index): 2.144574208,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.406795573,log10 matsuda insulin sensitivity index: 0.929288788,muscle mass (%): 40.2,lg10 serum c-reactive protein (mg/l): 0.505149978,lg10 plasma adiponectin (mg/l): 0.826074803,ogtt fasting plasma free fatty acid (mmol/l): 0.16,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 7.5,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.274781123,log10 il1 beta (pg/ml): -0.494850022,log10 ogtt fasting plasma insulin (mu/l): 0.633468456,ogtt 30 min plasma insulin (mu/l): 1.705863712,ogtt 120 min plasma insulin (mu/l): 1.565847819,log10 ogtt fasting plasma proinsulin (pm/l): 0.924279286,ogtt 30 min plasma proinsulin (pm/l): 1.387389826,ogtt 120 min plasma proinsulin (pm/l): 1.702430536,log10 bioimpedance: Resistance: 2.662757832,log10 bioimpedance (reactance): 1.591064607,waist to hip ratio: 0.923469388,log10 serum bilirubin (umol/l): 1.230448921,log10 serum alanine aminotransfrase (u/l): 1.531478917,log10 creatinine (umol/l): 1.84509804,log10 total cholesterol (mmol/l): 0.828659897,log10 ldl cholesterol (mmol/l): 0.62838893,log10 hdl cholesterol (mmol/l): 0.230448921,log10 total triglycerides (mmol/l): 0,log10 serum apoa1 (g/l): 0.193124598,log10 serum apob (g/l): 0.08278537,log10 urinary albumin excretion rate (ug/min): 0.776172684 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098335 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249234,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978162 | GSM1098335 | GSE45159 | 0.103856 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6051 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249234 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978162 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.411954731,log10 basal metabolic rate (kcal): 1526,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.506289531,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.534454111,plasma free fatty acids under the curve ogtt (mmol/l * min): 27.9,fat mass (%): 19.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.67507492,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 145.5,log10 homair (insulin resistance index based on homa): 0.364488457,log10 homais (insulin secretion index based on homa): 1.947293649,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.617660722,insgenin (insulinogenic index): 2.256586559,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.541167218,log10 matsuda insulin sensitivity index: 0.656212077,muscle mass (%): 45.2,lg10 serum c-reactive protein (mg/l): 0.079181246,lg10 plasma adiponectin (mg/l): 0.716003344,ogtt fasting plasma free fatty acid (mmol/l): 0.55,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 7.8,ogtt 120 min plasma glucose (mmol/l): 5.9,log10 il1 receptor antagonist (pg/ml): 2.49280228,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.968482949,ogtt 30 min plasma insulin (mu/l): 1.877946952,ogtt 120 min plasma insulin (mu/l): 1.697229343,log10 ogtt fasting plasma proinsulin (pm/l): 1.209515015,ogtt 30 min plasma proinsulin (pm/l): 1.629409599,ogtt 120 min plasma proinsulin (pm/l): 1.782472624,log10 bioimpedance: Resistance: 2.697229343,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 1,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.462397998,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.687528961,log10 ldl cholesterol (mmol/l): 0.439332694,log10 hdl cholesterol (mmol/l): 0.187520721,log10 total triglycerides (mmol/l): 0.064457989,log10 serum apoa1 (g/l): 0.173186268,log10 serum apob (g/l): -0.080921908,log10 urinary albumin excretion rate (ug/min): 1.279544106 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098336 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249235,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978163 | GSM1098336 | GSE45159 | 0.354039 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6083 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249235 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978163 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.445998957,log10 basal metabolic rate (kcal): 1725,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.485385281,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.86219625,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.35,fat mass (%): 19.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.924812504,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 204,log10 homair (insulin resistance index based on homa): -0.098844513,log10 homais (insulin secretion index based on homa): 1.285790029,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.004622266,insgenin (insulinogenic index): 1.382917135,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.908002201,log10 matsuda insulin sensitivity index: 1.160798768,muscle mass (%): 44.5,lg10 serum c-reactive protein (mg/l): -0.552841969,lg10 plasma adiponectin (mg/l): 0.995635195,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.2,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 10.4,ogtt 120 min plasma glucose (mmol/l): 5.6,log10 il1 receptor antagonist (pg/ml): 2.378107063,log10 il1 beta (pg/ml): -0.721246399,log10 ogtt fasting plasma insulin (mu/l): 0.447158031,ogtt 30 min plasma insulin (mu/l): 1.276461804,ogtt 120 min plasma insulin (mu/l): 1.053078443,log10 ogtt fasting plasma proinsulin (pm/l): 0.662757832,ogtt 30 min plasma proinsulin (pm/l): 1.056904851,ogtt 120 min plasma proinsulin (pm/l): 1.283301229,log10 bioimpedance: Resistance: 2.606381365,log10 bioimpedance (reactance): 1.568201724,waist to hip ratio: 0.956730769,log10 serum bilirubin (umol/l): 1.230448921,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.773054693,log10 ldl cholesterol (mmol/l): 0.506505032,log10 hdl cholesterol (mmol/l): 0.326335861,log10 total triglycerides (mmol/l): -0.050609993,log10 serum apoa1 (g/l): 0.245512668,log10 serum apob (g/l): -0.060480747,log10 urinary albumin excretion rate (ug/min): 0.702846328 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098337 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249236,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978164 | GSM1098337 | GSE45159 | 0.158657 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6101 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249236 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978164 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.354631945,log10 basal metabolic rate (kcal): 1731,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.945923049,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.958110157,plasma free fatty acids under the curve ogtt (mmol/l * min): 7.65,fat mass (%): 13.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.52160044,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 39,log10 homair (insulin resistance index based on homa): -0.0205528,log10 homais (insulin secretion index based on homa): 1.507503884,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.07415792,insgenin (insulinogenic index): 2.081150839,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.963693405,log10 matsuda insulin sensitivity index: 1.140861475,muscle mass (%): 51.2,lg10 serum c-reactive protein (mg/l): 0.427972714,lg10 plasma adiponectin (mg/l): 0.785329835,ogtt fasting plasma free fatty acid (mmol/l): 0.13,ogtt 30 min plasma free fatty acid (mmol/l): 0.08,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 6.9,ogtt 120 min plasma glucose (mmol/l): 5.2,log10 il1 receptor antagonist (pg/ml): 2.378361557,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.568201724,ogtt 30 min plasma insulin (mu/l): 1.411619706,ogtt 120 min plasma insulin (mu/l): 0.919078092,log10 ogtt fasting plasma proinsulin (pm/l): 0.851258349,ogtt 30 min plasma proinsulin (pm/l): 1.220108088,ogtt 120 min plasma proinsulin (pm/l): 1.305351369,log10 bioimpedance: Resistance: 2.651278014,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.95212766,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.176091259,log10 creatinine (umol/l): 1.799340549,log10 total cholesterol (mmol/l): 0.673020907,log10 ldl cholesterol (mmol/l): 0.503790683,log10 hdl cholesterol (mmol/l): 0.025305865,log10 total triglycerides (mmol/l): -0.031517051,log10 serum apoa1 (g/l): 0.075546961,log10 serum apob (g/l): 0.004321374,log10 urinary albumin excretion rate (ug/min): 0.701444624 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098338 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249237,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978165 | GSM1098338 | GSE45159 | 0.027879 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6183 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249237 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978165 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.403239499,log10 basal metabolic rate (kcal): 1629,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.569922884,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.560644292,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.9,fat mass (%): 17.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.716819461,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 169.5,log10 homair (insulin resistance index based on homa): 0.128399269,log10 homais (insulin secretion index based on homa): 1.711204461,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.384962397,insgenin (insulinogenic index): 1.862950873,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.309118932,log10 matsuda insulin sensitivity index: 0.888553184,muscle mass (%): 48.7,lg10 serum c-reactive protein (mg/l): -0.482804102,lg10 plasma adiponectin (mg/l): 0.681241237,ogtt fasting plasma free fatty acid (mmol/l): 0.23,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.8,ogtt 120 min plasma glucose (mmol/l): 5.1,log10 il1 receptor antagonist (pg/ml): 2.329194415,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.73239376,ogtt 30 min plasma insulin (mu/l): 1.646403726,ogtt 120 min plasma insulin (mu/l): 1.462397998,log10 ogtt fasting plasma proinsulin (pm/l): 0.949390007,ogtt 30 min plasma proinsulin (pm/l): 1.372912003,ogtt 120 min plasma proinsulin (pm/l): 1.57863921,log10 bioimpedance: Resistance: 2.657055853,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.917525773,log10 serum bilirubin (umol/l): 1.204119983,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.638489257,log10 ldl cholesterol (mmol/l): 0.477121255,log10 hdl cholesterol (mmol/l): -0.004364805,log10 total triglycerides (mmol/l): 0.120573931,log10 serum apoa1 (g/l): 0.075546961,log10 serum apob (g/l): 0,log10 urinary albumin excretion rate (ug/min): 0.821185883 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098339 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249238,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978166 | GSM1098339 | GSE45159 | 0.178675 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6200 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249238 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978166 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.472328633,log10 basal metabolic rate (kcal): 1784,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.475108188,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.954260854,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.5,fat mass (%): 23.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.964340868,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 195,log10 homair (insulin resistance index based on homa): 0.979042263,log10 homais (insulin secretion index based on homa): 2.301029996,log10 insulin area under the curve (ogtt) (pmol/l * min): 5.133564454,insgenin (insulinogenic index): 2.428801547,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 5.05295544,log10 matsuda insulin sensitivity index: 0.039439851,muscle mass (%): 43.2,lg10 serum c-reactive protein (mg/l): 0.573451822,lg10 plasma adiponectin (mg/l): 0.73239376,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.7,ogtt 30 min plasma glucose (mmol/l): 10.1,ogtt 120 min plasma glucose (mmol/l): 6.5,log10 il1 receptor antagonist (pg/ml): 2.265289626,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.505149978,ogtt 30 min plasma insulin (mu/l): 2.265053789,ogtt 120 min plasma insulin (mu/l): 2.39375064,log10 ogtt fasting plasma proinsulin (pm/l): 1.426511261,ogtt 30 min plasma proinsulin (pm/l): 1.742725131,ogtt 120 min plasma proinsulin (pm/l): 1.950364854,log10 bioimpedance: Resistance: 2.627365857,log10 bioimpedance (reactance): 1.62324929,waist to hip ratio: 1.009478673,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.781755375,log10 ldl cholesterol (mmol/l): 0.591064607,log10 hdl cholesterol (mmol/l): 0.123851641,log10 total triglycerides (mmol/l): 0.004321374,log10 serum apoa1 (g/l): 0.100370545,log10 serum apob (g/l): 0,log10 urinary albumin excretion rate (ug/min): 0.718224804 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098340 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249239,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978167 | GSM1098340 | GSE45159 | 0.104108 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6283 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249239 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978167 |
|
1 | age: 67,tissue: adipose tissue,log10 body mass index: 1.43877661,log10 basal metabolic rate (kcal): 1618,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.353567711,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.519040794,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.5,fat mass (%): 28.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.897845456,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 198,log10 homair (insulin resistance index based on homa): 0.561101384,log10 homais (insulin secretion index based on homa): 1.967815317,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.587003398,insgenin (insulinogenic index): 2.012837225,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.466526573,log10 matsuda insulin sensitivity index: 0.526049836,muscle mass (%): 37.7,lg10 serum c-reactive protein (mg/l): 0.666705136,lg10 plasma adiponectin (mg/l): 1.045322979,ogtt fasting plasma free fatty acid (mmol/l): 0.3,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 6.3,ogtt 30 min plasma glucose (mmol/l): 8.7,ogtt 120 min plasma glucose (mmol/l): 7.5,log10 il1 receptor antagonist (pg/ml): 2.428361605,log10 il1 beta (pg/ml): 0.053078443,log10 ogtt fasting plasma insulin (mu/l): 1.113943352,ogtt 30 min plasma insulin (mu/l): 1.733999287,ogtt 120 min plasma insulin (mu/l): 1.822821645,log10 ogtt fasting plasma proinsulin (pm/l): 1.113943352,ogtt 30 min plasma proinsulin (pm/l): 1.33243846,ogtt 120 min plasma proinsulin (pm/l): 1.69019608,log10 bioimpedance: Resistance: 2.650307523,log10 bioimpedance (reactance): 1.612783857,waist to hip ratio: 0.980952381,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.934498451,log10 total cholesterol (mmol/l): 0.691081492,log10 ldl cholesterol (mmol/l): 0.488550717,log10 hdl cholesterol (mmol/l): 0.146128036,log10 total triglycerides (mmol/l): -0.026872146,log10 serum apoa1 (g/l): 0.139879086,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 1.605445587 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098341 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249240,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978168 | GSM1098341 | GSE45159 | 0.24973 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6419 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249240 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978168 |
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1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.402831425,log10 basal metabolic rate (kcal): 1673,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.475108188,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.738992868,plasma free fatty acids under the curve ogtt (mmol/l * min): 6.75,fat mass (%): 20.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.67507492,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 73.5,log10 homair (insulin resistance index based on homa): 0.315270435,log10 homais (insulin secretion index based on homa): 1.744727495,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.544638457,insgenin (insulinogenic index): 2.523346195,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.471966104,log10 matsuda insulin sensitivity index: 0.722676048,muscle mass (%): 44.1,lg10 serum c-reactive protein (mg/l): -0.071604148,lg10 plasma adiponectin (mg/l): 0.982271233,ogtt fasting plasma free fatty acid (mmol/l): 0.19,ogtt 30 min plasma free fatty acid (mmol/l): 0.05,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6.2,ogtt 30 min plasma glucose (mmol/l): 7.5,ogtt 120 min plasma glucose (mmol/l): 6.1,log10 il1 receptor antagonist (pg/ml): 2.137955124,log10 il1 beta (pg/ml): -0.013228266,log10 ogtt fasting plasma insulin (mu/l): 0.875061263,ogtt 30 min plasma insulin (mu/l): 1.902002891,ogtt 120 min plasma insulin (mu/l): 1.320146286,log10 ogtt fasting plasma proinsulin (pm/l): 1.075546961,ogtt 30 min plasma proinsulin (pm/l): 1.434568904,ogtt 120 min plasma proinsulin (pm/l): 1.414973348,log10 bioimpedance: Resistance: 2.692846919,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.955665025,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.230448921,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.666517981,log10 ldl cholesterol (mmol/l): 0.436162647,log10 hdl cholesterol (mmol/l): 0.195899652,log10 total triglycerides (mmol/l): -0.055517328,log10 serum apoa1 (g/l): 0.173186268,log10 serum apob (g/l): -0.080921908,log10 urinary albumin excretion rate (ug/min): 0.949186638 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098342 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249241,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978169 | GSM1098342 | GSE45159 | 0.204272 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6433 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249241 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978169 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.419899053,log10 basal metabolic rate (kcal): 1821,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.601836376,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.994353345,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.1,fat mass (%): 21.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.767356854,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 247.5,log10 homair (insulin resistance index based on homa): -0.131029196,log10 homais (insulin secretion index based on homa): 1.575731053,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.3029367,insgenin (insulinogenic index): 1.731499229,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.25002945,log10 matsuda insulin sensitivity index: 1.081966087,muscle mass (%): 46.3,lg10 serum c-reactive protein (mg/l): 0.345961542,lg10 plasma adiponectin (mg/l): 0.643452676,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 10.6,ogtt 120 min plasma glucose (mmol/l): 3.5,log10 il1 receptor antagonist (pg/ml): 2.435573644,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.505149978,ogtt 30 min plasma insulin (mu/l): 1.713490543,ogtt 120 min plasma insulin (mu/l): 0.643452676,log10 ogtt fasting plasma proinsulin (pm/l): 1.008600172,ogtt 30 min plasma proinsulin (pm/l): 1.463892989,ogtt 120 min plasma proinsulin (pm/l): 1.372912003,log10 bioimpedance: Resistance: 2.683047038,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 1,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.361727836,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.88422877,log10 ldl cholesterol (mmol/l): 0.720159303,log10 hdl cholesterol (mmol/l): 0.149219113,log10 total triglycerides (mmol/l): 0.238046103,log10 serum apoa1 (g/l): 0.152288344,log10 serum apob (g/l): 0.190331698,log10 urinary albumin excretion rate (ug/min): 0.711872093 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098343 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249242,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978170 | GSM1098343 | GSE45159 | 0.271206 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6484 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249242 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978170 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.536341392,log10 basal metabolic rate (kcal): 1485,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.957409505,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.504109502,plasma free fatty acids under the curve ogtt (mmol/l * min): 46.65,fat mass (%): 30.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.983706193,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 388.5,log10 homair (insulin resistance index based on homa): -0.002710719,log10 homais (insulin secretion index based on homa): 1.70404953,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.394521723,insgenin (insulinogenic index): 1.685936359,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.336619813,log10 matsuda insulin sensitivity index: 0.915125661,muscle mass (%): 37.6,lg10 serum c-reactive protein (mg/l): 0.949194774,lg10 plasma adiponectin (mg/l): 0.838849091,ogtt fasting plasma free fatty acid (mmol/l): 0.56,ogtt 30 min plasma free fatty acid (mmol/l): 0.51,ogtt 120 min plasma free fatty acid (mmol/l): 0.17,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 9.8,ogtt 120 min plasma glucose (mmol/l): 7.7,log10 il1 receptor antagonist (pg/ml): 2.691991583,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.633468456,ogtt 30 min plasma insulin (mu/l): 1.618048097,ogtt 120 min plasma insulin (mu/l): 1.545307116,log10 ogtt fasting plasma proinsulin (pm/l): 1.206825876,ogtt 30 min plasma proinsulin (pm/l): 1.6599162,ogtt 120 min plasma proinsulin (pm/l): 1.960470778,log10 bioimpedance: Resistance: 2.720985744,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 1.068965517,log10 serum bilirubin (umol/l): 0.954242509,log10 serum alanine aminotransfrase (u/l): 1.913813852,log10 creatinine (umol/l): 1.799340549,log10 total cholesterol (mmol/l): 0.73239376,log10 ldl cholesterol (mmol/l): 0.354108439,log10 hdl cholesterol (mmol/l): 0.456366033,log10 total triglycerides (mmol/l): -0.142667504,log10 serum apoa1 (g/l): 0.292256071,log10 serum apob (g/l): -0.180456064,log10 urinary albumin excretion rate (ug/min): 0.872541066 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098344 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249243,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978171 | GSM1098344 | GSE45159 | 0.297086 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6515 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249243 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978171 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.388282902,log10 basal metabolic rate (kcal): 1782,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.636085368,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.826376616,plasma free fatty acids under the curve ogtt (mmol/l * min): 14.7,fat mass (%): 18.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.742309436,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 184.5,log10 homair (insulin resistance index based on homa): 0.077246746,log10 homais (insulin secretion index based on homa): 1.660051938,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.344824388,insgenin (insulinogenic index): 1.925753972,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.271051261,log10 matsuda insulin sensitivity index: 0.920724689,muscle mass (%): 46.8,lg10 serum c-reactive protein (mg/l): 0.630020851,lg10 plasma adiponectin (mg/l): 0.86923172,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 7.7,ogtt 120 min plasma glucose (mmol/l): 6.9,log10 il1 receptor antagonist (pg/ml): 2.439064138,log10 il1 beta (pg/ml): -0.251811973,log10 ogtt fasting plasma insulin (mu/l): 0.681241237,ogtt 30 min plasma insulin (mu/l): 1.53529412,ogtt 120 min plasma insulin (mu/l): 1.539076099,log10 ogtt fasting plasma proinsulin (pm/l): 1.075546961,ogtt 30 min plasma proinsulin (pm/l): 1.481442629,ogtt 120 min plasma proinsulin (pm/l): 1.747411808,log10 bioimpedance: Resistance: 2.671172843,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 0.912037037,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.612783857,log10 creatinine (umol/l): 1.86923172,log10 total cholesterol (mmol/l): 0.597695186,log10 ldl cholesterol (mmol/l): 0.392696953,log10 hdl cholesterol (mmol/l): 0.068185862,log10 total triglycerides (mmol/l): 0.025305865,log10 serum apoa1 (g/l): 0.045322979,log10 serum apob (g/l): -0.124938737,log10 urinary albumin excretion rate (ug/min): 0.952076448 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098345 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249244,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978172 | GSM1098345 | GSE45159 | 0.297942 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6517 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249244 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978172 |
|
1 | age: 47,tissue: adipose tissue,log10 body mass index: 1.481963825,log10 basal metabolic rate (kcal): 2001,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.419127718,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.195955526,plasma free fatty acids under the curve ogtt (mmol/l * min): 9.3,fat mass (%): 25.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.82336724,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 234,log10 homair (insulin resistance index based on homa): 0.417194808,log10 homais (insulin secretion index based on homa): 2,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.708514378,insgenin (insulinogenic index): 2.243864489,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.638998132,log10 matsuda insulin sensitivity index: 0.56431174,muscle mass (%): 43.5,lg10 serum c-reactive protein (mg/l): 1.608547427,lg10 plasma adiponectin (mg/l): 0.785329835,ogtt fasting plasma free fatty acid (mmol/l): 0.32,ogtt 30 min plasma free fatty acid (mmol/l): 0.03,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.3,ogtt 120 min plasma glucose (mmol/l): 7.2,log10 il1 receptor antagonist (pg/ml): 2.299834041,log10 il1 beta (pg/ml): -0.721246399,log10 ogtt fasting plasma insulin (mu/l): 1.021189299,ogtt 30 min plasma insulin (mu/l): 1.951337519,ogtt 120 min plasma insulin (mu/l): 1.823474229,log10 ogtt fasting plasma proinsulin (pm/l): 0.963787827,ogtt 30 min plasma proinsulin (pm/l): 1.505149978,ogtt 120 min plasma proinsulin (pm/l): 1.935507266,log10 bioimpedance: Resistance: 2.650307523,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.99047619,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.698100546,log10 ldl cholesterol (mmol/l): 0.494154594,log10 hdl cholesterol (mmol/l): 0.149219113,log10 total triglycerides (mmol/l): -0.036212173,log10 serum apoa1 (g/l): 0.079181246,log10 serum apob (g/l): -0.050609993,log10 urinary albumin excretion rate (ug/min): 0.927913571 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098346 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249245,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978173 | GSM1098346 | GSE45159 | 0.237383 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6557 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249245 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978173 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.434099733,log10 basal metabolic rate (kcal): 1761,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.322656165,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.706372582,plasma free fatty acids under the curve ogtt (mmol/l * min): 18,fat mass (%): 22.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.842350343,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 198,log10 homair (insulin resistance index based on homa): 0.553073531,log10 homais (insulin secretion index based on homa): 2.030194785,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.915378727,insgenin (insulinogenic index): 2.378397901,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.861223663,log10 matsuda insulin sensitivity index: 0.406122096,muscle mass (%): 45.3,lg10 serum c-reactive protein (mg/l): 0.345961542,lg10 plasma adiponectin (mg/l): 0.785329835,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.2,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 10.2,ogtt 120 min plasma glucose (mmol/l): 4.8,log10 il1 receptor antagonist (pg/ml): 2.239024047,log10 il1 beta (pg/ml): -0.37675071,log10 ogtt fasting plasma insulin (mu/l): 1.127104798,ogtt 30 min plasma insulin (mu/l): 2.256958153,ogtt 120 min plasma insulin (mu/l): 1.773786445,log10 ogtt fasting plasma proinsulin (pm/l): 1.478566496,ogtt 30 min plasma proinsulin (pm/l): 1.864511081,ogtt 120 min plasma proinsulin (pm/l): 2.086359831,log10 bioimpedance: Resistance: 2.69019608,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 0.953271028,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.698970004,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.716003344,log10 ldl cholesterol (mmol/l): 0.519827994,log10 hdl cholesterol (mmol/l): 0.089905111,log10 total triglycerides (mmol/l): 0.089905111,log10 serum apoa1 (g/l): 0.089905111,log10 serum apob (g/l): 0.004321374,log10 urinary albumin excretion rate (ug/min): 0.70775937 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098347 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249246,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978174 | GSM1098347 | GSE45159 | 0.050975 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6572 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249246 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978174 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.374261909,log10 basal metabolic rate (kcal): 1460,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.951609967,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.974411969,plasma free fatty acids under the curve ogtt (mmol/l * min): 23.7,fat mass (%): 17.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.784634846,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 174,log10 homair (insulin resistance index based on homa): 0.081427325,log10 homais (insulin secretion index based on homa): 1.583576586,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.025018972,insgenin (insulinogenic index): 1.273914615,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.862191031,log10 matsuda insulin sensitivity index: 1.0683719,muscle mass (%): 44.4,lg10 serum c-reactive protein (mg/l): 0.220369632,lg10 plasma adiponectin (mg/l): 0.875061263,ogtt fasting plasma free fatty acid (mmol/l): 0.42,ogtt 30 min plasma free fatty acid (mmol/l): 0.26,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 9.7,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.076021142,log10 il1 beta (pg/ml): -0.408935393,log10 ogtt fasting plasma insulin (mu/l): 0.662757832,ogtt 30 min plasma insulin (mu/l): 1.217483944,ogtt 120 min plasma insulin (mu/l): 1.195899652,log10 ogtt fasting plasma proinsulin (pm/l): 0.913813852,ogtt 30 min plasma proinsulin (pm/l): 1.089905111,ogtt 120 min plasma proinsulin (pm/l): 1.356025857,log10 bioimpedance: Resistance: 2.709269961,log10 bioimpedance (reactance): 1.653212514,waist to hip ratio: 0.958333333,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.342422681,log10 creatinine (umol/l): 1.799340549,log10 total cholesterol (mmol/l): 0.716837723,log10 ldl cholesterol (mmol/l): 0.471291711,log10 hdl cholesterol (mmol/l): 0.158362492,log10 total triglycerides (mmol/l): -0.036212173,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 0.524762889 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098348 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249247,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978175 | GSM1098348 | GSE45159 | 0.447861 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6589 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249247 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978175 |
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1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.455751037,log10 basal metabolic rate (kcal): 1704,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.678942752,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.890859659,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.15,fat mass (%): 16.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.547858506,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 52.5,log10 homair (insulin resistance index based on homa): 0.375033303,log10 homais (insulin secretion index based on homa): 1.903089987,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.462502815,insgenin (insulinogenic index): 2.206667172,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.349918295,log10 matsuda insulin sensitivity index: 0.741058136,muscle mass (%): 47.8,lg10 serum c-reactive protein (mg/l): 0.038620162,lg10 plasma adiponectin (mg/l): 0.643452676,ogtt fasting plasma free fatty acid (mmol/l): 0.27,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 7.5,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.338277161,log10 il1 beta (pg/ml): -0.508638306,log10 ogtt fasting plasma insulin (mu/l): 0.963787827,ogtt 30 min plasma insulin (mu/l): 1.738780558,ogtt 120 min plasma insulin (mu/l): 1.495544338,log10 ogtt fasting plasma proinsulin (pm/l): 1.086359831,ogtt 30 min plasma proinsulin (pm/l): 1.371067862,ogtt 120 min plasma proinsulin (pm/l): 1.682145076,log10 bioimpedance: Resistance: 2.545307116,log10 bioimpedance (reactance): 1.556302501,waist to hip ratio: 1.072164948,log10 serum bilirubin (umol/l): 0.903089987,log10 serum alanine aminotransfrase (u/l): 1.544068044,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.756636108,log10 ldl cholesterol (mmol/l): 0.574031268,log10 hdl cholesterol (mmol/l): -0.193820026,log10 total triglycerides (mmol/l): 0.509202522,log10 serum apoa1 (g/l): 0.008600172,log10 serum apob (g/l): 0.187520721,log10 urinary albumin excretion rate (ug/min): 0.669006781 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098349 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249248,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978176 | GSM1098349 | GSE45159 | 0.23117 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6611 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249248 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978176 |
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1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.473982303,log10 basal metabolic rate (kcal): 1644,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.498395033,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.005320074,plasma free fatty acids under the curve ogtt (mmol/l * min): 32.4,fat mass (%): 25.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.02375435,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 357,log10 homair (insulin resistance index based on homa): 0.29578694,log10 homais (insulin secretion index based on homa): 1.850701918,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.860954566,insgenin (insulinogenic index): 2.184691431,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.825990528,log10 matsuda insulin sensitivity index: 0.535886342,muscle mass (%): 41.5,lg10 serum c-reactive protein (mg/l): 0.506775537,lg10 plasma adiponectin (mg/l): 0.544068044,ogtt fasting plasma free fatty acid (mmol/l): 0.45,ogtt 30 min plasma free fatty acid (mmol/l): 0.39,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 10.9,ogtt 120 min plasma glucose (mmol/l): 6.7,log10 il1 receptor antagonist (pg/ml): 2.372599051,log10 il1 beta (pg/ml): 0.354108439,log10 ogtt fasting plasma insulin (mu/l): 0.892094603,ogtt 30 min plasma insulin (mu/l): 2.147367108,ogtt 120 min plasma insulin (mu/l): 1.898176483,log10 ogtt fasting plasma proinsulin (pm/l): 1.029383778,ogtt 30 min plasma proinsulin (pm/l): 1.680335513,ogtt 120 min plasma proinsulin (pm/l): 1.92890769,log10 bioimpedance: Resistance: 2.701567985,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 1,log10 serum bilirubin (umol/l): 1.491361694,log10 serum alanine aminotransfrase (u/l): 1.62324929,log10 creatinine (umol/l): 1.919078092,log10 total cholesterol (mmol/l): 0.763427994,log10 ldl cholesterol (mmol/l): 0.57863921,log10 hdl cholesterol (mmol/l): 0.152288344,log10 total triglycerides (mmol/l): 0.164352856,log10 serum apoa1 (g/l): 0.181843588,log10 serum apob (g/l): 0.10720997,log10 urinary albumin excretion rate (ug/min): 0.961603609 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098350 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249249,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978177 | GSM1098350 | GSE45159 | 0.188003 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6648 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249249 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978177 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.470951159,log10 basal metabolic rate (kcal): 1748,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.879959722,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.19471946,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.55,fat mass (%): 24.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.77478706,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 72,log10 homair (insulin resistance index based on homa): 0.437680112,log10 homais (insulin secretion index based on homa): 1.759667845,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.751440779,insgenin (insulinogenic index): 2.588511803,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.69720318,log10 matsuda insulin sensitivity index: 0.554709764,muscle mass (%): 46.6,lg10 serum c-reactive protein (mg/l): 0.566437492,lg10 plasma adiponectin (mg/l): 0.944482672,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 6.7,ogtt 30 min plasma glucose (mmol/l): 8.8,ogtt 120 min plasma glucose (mmol/l): 5.5,log10 il1 receptor antagonist (pg/ml): 2.447344118,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.963787827,ogtt 30 min plasma insulin (mu/l): 2.161068385,ogtt 120 min plasma insulin (mu/l): 1.103803721,log10 ogtt fasting plasma proinsulin (pm/l): 1.08278537,ogtt 30 min plasma proinsulin (pm/l): 1.546542663,ogtt 120 min plasma proinsulin (pm/l): 1.408239965,log10 bioimpedance: Resistance: 2.686636269,log10 bioimpedance (reactance): 1.86923172,waist to hip ratio: 0.990384615,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 1.819543936,log10 total cholesterol (mmol/l): 0.656098202,log10 ldl cholesterol (mmol/l): 0.478566496,log10 hdl cholesterol (mmol/l): 0.167317335,log10 total triglycerides (mmol/l): -0.229147988,log10 serum apoa1 (g/l): 0.127104798,log10 serum apob (g/l): -0.075720714,log10 urinary albumin excretion rate (ug/min): 1.079181246 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098351 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249250,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978178 | GSM1098351 | GSE45159 | 0.161131 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6664 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249250 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978178 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.451543353,log10 basal metabolic rate (kcal): 1792,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.492595495,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.047795062,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.45,fat mass (%): 24.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.789533645,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 189,log10 homair (insulin resistance index based on homa): 0.280477195,log10 homais (insulin secretion index based on homa): 1.808533879,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.609573067,insgenin (insulinogenic index): 2.199343719,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.54863506,log10 matsuda insulin sensitivity index: 0.686035817,muscle mass (%): 42.7,lg10 serum c-reactive protein (mg/l): 0.293141483,lg10 plasma adiponectin (mg/l): 0.812913357,ogtt fasting plasma free fatty acid (mmol/l): 0.26,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 8.2,ogtt 120 min plasma glucose (mmol/l): 6.8,log10 il1 receptor antagonist (pg/ml): 2.485139138,log10 il1 beta (pg/ml): -0.886056648,log10 ogtt fasting plasma insulin (mu/l): 0.86923172,ogtt 30 min plasma insulin (mu/l): 1.849419414,ogtt 120 min plasma insulin (mu/l): 1.73239376,log10 ogtt fasting plasma proinsulin (pm/l): 1.075546961,ogtt 30 min plasma proinsulin (pm/l): 1.46686762,ogtt 120 min plasma proinsulin (pm/l): 1.7084209,log10 bioimpedance: Resistance: 2.697229343,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 1.037383178,log10 serum bilirubin (umol/l): 1.477121255,log10 serum alanine aminotransfrase (u/l): 1.826074803,log10 creatinine (umol/l): 1.919078092,log10 total cholesterol (mmol/l): 0.638489257,log10 ldl cholesterol (mmol/l): 0.409933123,log10 hdl cholesterol (mmol/l): 0.075546961,log10 total triglycerides (mmol/l): 0.130333768,log10 serum apoa1 (g/l): 0.103803721,log10 serum apob (g/l): -0.055517328,log10 urinary albumin excretion rate (ug/min): 0.865728042 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098352 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249251,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978179 | GSM1098352 | GSE45159 | 0.301818 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6671 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249251 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978179 |
|
1 | age: 46,tissue: adipose tissue,log10 body mass index: 1.425726864,log10 basal metabolic rate (kcal): 1645,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.50287596,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.64814536,plasma free fatty acids under the curve ogtt (mmol/l * min): 7.8,fat mass (%): 17.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.35645197,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): -64.5,log10 homair (insulin resistance index based on homa): -0.082669574,log10 homais (insulin secretion index based on homa): 1.394451681,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.190527787,insgenin (insulinogenic index): 2.403977964,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.12303453,log10 matsuda insulin sensitivity index: 1.144027476,muscle mass (%): 50.3,lg10 serum c-reactive protein (mg/l): -0.485452247,lg10 plasma adiponectin (mg/l): 0.886490725,ogtt fasting plasma free fatty acid (mmol/l): 0.18,ogtt 30 min plasma free fatty acid (mmol/l): 0.07,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 6.8,ogtt 120 min plasma glucose (mmol/l): 3.5,log10 il1 receptor antagonist (pg/ml): 2.199535781,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.491361694,ogtt 30 min plasma insulin (mu/l): 1.567026366,ogtt 120 min plasma insulin (mu/l): 0.857332496,log10 ogtt fasting plasma proinsulin (pm/l): 1.146128036,ogtt 30 min plasma proinsulin (pm/l): 1.383815366,ogtt 120 min plasma proinsulin (pm/l): 1.357934847,log10 bioimpedance: Resistance: 2.631443769,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 0.974226804,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.176091259,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.720159303,log10 ldl cholesterol (mmol/l): 0.521138084,log10 hdl cholesterol (mmol/l): 0.260071388,log10 total triglycerides (mmol/l): -0.13667714,log10 serum apoa1 (g/l): 0.193124598,log10 serum apob (g/l): -0.017728767,log10 urinary albumin excretion rate (ug/min): 0.990739639 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098353 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249252,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978180 | GSM1098353 | GSE45159 | 0.083802 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6675 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249252 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978180 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.478205327,log10 basal metabolic rate (kcal): 1978,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.472656693,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.134352882,plasma free fatty acids under the curve ogtt (mmol/l * min): 23.55,fat mass (%): 24,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.04234338,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 286.5,log10 homair (insulin resistance index based on homa): 0.853671177,log10 homais (insulin secretion index based on homa): 2.238305719,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.985812542,insgenin (insulinogenic index): 2.30786474,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.896051982,log10 matsuda insulin sensitivity index: 0.161516111,muscle mass (%): 44.6,lg10 serum c-reactive protein (mg/l): 0.311329952,lg10 plasma adiponectin (mg/l): 0.591064607,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.27,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 8.9,log10 il1 receptor antagonist (pg/ml): 2.696478708,log10 il1 beta (pg/ml): 0.544068044,log10 ogtt fasting plasma insulin (mu/l): 1.399673721,ogtt 30 min plasma insulin (mu/l): 2.090963077,ogtt 120 min plasma insulin (mu/l): 2.268811904,log10 ogtt fasting plasma proinsulin (pm/l): 1.641474111,ogtt 30 min plasma proinsulin (pm/l): 1.868644438,ogtt 120 min plasma proinsulin (pm/l): 1.957128198,log10 bioimpedance: Resistance: 2.625312451,log10 bioimpedance (reactance): 1.69019608,waist to hip ratio: 1.01843318,log10 serum bilirubin (umol/l): 0.84509804,log10 serum alanine aminotransfrase (u/l): 1.612783857,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.751279104,log10 ldl cholesterol (mmol/l): 0.579783597,log10 hdl cholesterol (mmol/l): 0.021189299,log10 total triglycerides (mmol/l): 0.294466226,log10 serum apoa1 (g/l): 0.120573931,log10 serum apob (g/l): 0.127104798,log10 urinary albumin excretion rate (ug/min): 0.81957659 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098354 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249253,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978181 | GSM1098354 | GSE45159 | 0.203916 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6680 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249253 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978181 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.476050203,log10 basal metabolic rate (kcal): 1815,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.199113459,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.749756497,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.65,fat mass (%): 23.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.913637428,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 184.5,log10 homair (insulin resistance index based on homa): 0.246060674,log10 homais (insulin secretion index based on homa): 1.609238576,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.111699278,insgenin (insulinogenic index): 1.463757293,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.931508722,log10 matsuda insulin sensitivity index: 0.921968465,muscle mass (%): 44.8,lg10 serum c-reactive protein (mg/l): -0.322393047,lg10 plasma adiponectin (mg/l): 1.149219113,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 6.5,ogtt 30 min plasma glucose (mmol/l): 9.8,ogtt 120 min plasma glucose (mmol/l): 6.2,log10 il1 receptor antagonist (pg/ml): 2.261691003,log10 il1 beta (pg/ml): 0.10720997,log10 ogtt fasting plasma insulin (mu/l): 0.785329835,ogtt 30 min plasma insulin (mu/l): 1.344392274,ogtt 120 min plasma insulin (mu/l): 1.214843848,log10 ogtt fasting plasma proinsulin (pm/l): 1.139879086,ogtt 30 min plasma proinsulin (pm/l): 1.238046103,ogtt 120 min plasma proinsulin (pm/l): 1.45331834,log10 bioimpedance: Resistance: 2.639486489,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.95045045,log10 serum bilirubin (umol/l): 1.397940009,log10 serum alanine aminotransfrase (u/l): 1.77815125,log10 creatinine (umol/l): 1.995635195,log10 total cholesterol (mmol/l): 0.757396029,log10 ldl cholesterol (mmol/l): 0.50242712,log10 hdl cholesterol (mmol/l): 0.328379603,log10 total triglycerides (mmol/l): -0.017728767,log10 serum apoa1 (g/l): 0.294466226,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 0.910038847 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098355 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249254,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978182 | GSM1098355 | GSE45159 | 0.228382 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6684 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249254 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978182 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.477263882,log10 basal metabolic rate (kcal): 1941,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.309001269,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.899795349,plasma free fatty acids under the curve ogtt (mmol/l * min): 35.7,fat mass (%): 21.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.924812504,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 252,log10 homair (insulin resistance index based on homa): 0.421603927,log10 homais (insulin secretion index based on homa): 1.898725182,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.342343711,insgenin (insulinogenic index): 1.693140461,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.172252552,log10 matsuda insulin sensitivity index: 0.722590609,muscle mass (%): 46.5,lg10 serum c-reactive protein (mg/l): 0.670060217,lg10 plasma adiponectin (mg/l): 0.643452676,ogtt fasting plasma free fatty acid (mmol/l): 0.61,ogtt 30 min plasma free fatty acid (mmol/l): 0.36,ogtt 120 min plasma free fatty acid (mmol/l): 0.11,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 9.6,ogtt 120 min plasma glucose (mmol/l): 6.8,log10 il1 receptor antagonist (pg/ml): 2.294686624,log10 il1 beta (pg/ml): -0.585026652,log10 ogtt fasting plasma insulin (mu/l): 0.995635195,ogtt 30 min plasma insulin (mu/l): 1.596597096,ogtt 120 min plasma insulin (mu/l): 1.40654018,log10 ogtt fasting plasma proinsulin (pm/l): 1.303196057,ogtt 30 min plasma proinsulin (pm/l): 1.46834733,ogtt 120 min plasma proinsulin (pm/l): 1.625312451,log10 bioimpedance: Resistance: 2.586587305,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.981308411,log10 serum bilirubin (umol/l): 1.477121255,log10 serum alanine aminotransfrase (u/l): 1.633468456,log10 creatinine (umol/l): 1.968482949,log10 total cholesterol (mmol/l): 0.745074792,log10 ldl cholesterol (mmol/l): 0.565847819,log10 hdl cholesterol (mmol/l): 0.041392685,log10 total triglycerides (mmol/l): 0.292256071,log10 serum apoa1 (g/l): 0.123851641,log10 serum apob (g/l): 0.117271296,log10 urinary albumin excretion rate (ug/min): 1.159401226 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098356 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249255,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978183 | GSM1098356 | GSE45159 | 0.225891 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6725 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249255 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978183 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.470086234,log10 basal metabolic rate (kcal): 1851,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.452953858,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.901550678,plasma free fatty acids under the curve ogtt (mmol/l * min): 23.7,fat mass (%): 21.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.794415866,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 180,log10 homair (insulin resistance index based on homa): 0.03145335,log10 homais (insulin secretion index based on homa): 1.533602611,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.595220567,insgenin (insulinogenic index): 2.484299839,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.561375714,log10 matsuda insulin sensitivity index: 0.83435416,muscle mass (%): 47.2,lg10 serum c-reactive protein (mg/l): -0.583359493,lg10 plasma adiponectin (mg/l): 1.008600172,ogtt fasting plasma free fatty acid (mmol/l): 0.29,ogtt 30 min plasma free fatty acid (mmol/l): 0.24,ogtt 120 min plasma free fatty acid (mmol/l): 0.11,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 7.7,ogtt 120 min plasma glucose (mmol/l): 7.5,log10 il1 receptor antagonist (pg/ml): 2.256693698,log10 il1 beta (pg/ml): -0.214670165,log10 ogtt fasting plasma insulin (mu/l): 0.612783857,ogtt 30 min plasma insulin (mu/l): 1.980457892,ogtt 120 min plasma insulin (mu/l): 1.230448921,log10 ogtt fasting plasma proinsulin (pm/l): 0.939519253,ogtt 30 min plasma proinsulin (pm/l): 1.459392488,ogtt 120 min plasma proinsulin (pm/l): 1.376576957,log10 bioimpedance: Resistance: 2.605305046,log10 bioimpedance (reactance): 1.707570176,waist to hip ratio: 0.906542056,log10 serum bilirubin (umol/l): 1.322219295,log10 serum alanine aminotransfrase (u/l): 1.51851394,log10 creatinine (umol/l): 1.929418926,log10 total cholesterol (mmol/l): 0.691081492,log10 ldl cholesterol (mmol/l): 0.460897843,log10 hdl cholesterol (mmol/l): 0.243038049,log10 total triglycerides (mmol/l): -0.292429824,log10 serum apoa1 (g/l): 0.152288344,log10 serum apob (g/l): -0.113509275,log10 urinary albumin excretion rate (ug/min): 1.365487985 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098357 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249256,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978184 | GSM1098357 | GSE45159 | 0.345112 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6741 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249256 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978184 |
|
1 | age: 53,tissue: adipose tissue,log10 body mass index: 1.432217682,log10 basal metabolic rate (kcal): 1582,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.966982949,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.115713435,plasma free fatty acids under the curve ogtt (mmol/l * min): 11.25,fat mass (%): 20.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.782179194,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 184.5,log10 homair (insulin resistance index based on homa): 0.335524762,log10 homais (insulin secretion index based on homa): 1.863581446,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.664190526,insgenin (insulinogenic index): 2.249931757,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.603187692,log10 matsuda insulin sensitivity index: 0.642786189,muscle mass (%): 45.1,lg10 serum c-reactive protein (mg/l): 0.207365037,lg10 plasma adiponectin (mg/l): 0.939519253,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.11,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 8.8,ogtt 120 min plasma glucose (mmol/l): 5.9,log10 il1 receptor antagonist (pg/ml): 2.140036411,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.924279286,ogtt 30 min plasma insulin (mu/l): 1.98811284,ogtt 120 min plasma insulin (mu/l): 1.584331224,log10 ogtt fasting plasma proinsulin (pm/l): 1.488550717,ogtt 30 min plasma proinsulin (pm/l): 1.761927838,ogtt 120 min plasma proinsulin (pm/l): 1.873320602,log10 bioimpedance: Resistance: 2.680335513,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 1.02020202,log10 serum bilirubin (umol/l): 0.954242509,log10 serum alanine aminotransfrase (u/l): 1.544068044,log10 creatinine (umol/l): 1.792391689,log10 total cholesterol (mmol/l): 0.716003344,log10 ldl cholesterol (mmol/l): 0.487138375,log10 hdl cholesterol (mmol/l): 0.26245109,log10 total triglycerides (mmol/l): -0.055517328,log10 serum apoa1 (g/l): 0.193124598,log10 serum apob (g/l): -0.040958608,log10 urinary albumin excretion rate (ug/min): 0.86232778 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098358 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249257,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978185 | GSM1098358 | GSE45159 | 0.264122 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6781 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249257 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978185 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.533768088,log10 basal metabolic rate (kcal): 2041,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.507089067,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.375208909,plasma free fatty acids under the curve ogtt (mmol/l * min): 32.7,fat mass (%): 29,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.902375114,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 225,log10 homair (insulin resistance index based on homa): 0.560252115,log10 homais (insulin secretion index based on homa): 2.013161446,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.658736206,insgenin (insulinogenic index): 2.082186756,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.555433042,log10 matsuda insulin sensitivity index: 0.506696474,muscle mass (%): 41.8,lg10 serum c-reactive protein (mg/l): 0.472756449,lg10 plasma adiponectin (mg/l): 0.602059991,ogtt fasting plasma free fatty acid (mmol/l): 0.33,ogtt 30 min plasma free fatty acid (mmol/l): 0.41,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 6.1,ogtt 30 min plasma glucose (mmol/l): 9.7,ogtt 120 min plasma glucose (mmol/l): 6.3,log10 il1 receptor antagonist (pg/ml): 2.246818521,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.127104798,ogtt 30 min plasma insulin (mu/l): 1.933993164,ogtt 120 min plasma insulin (mu/l): 1.697229343,log10 ogtt fasting plasma proinsulin (pm/l): 1.361727836,ogtt 30 min plasma proinsulin (pm/l): 1.681241237,ogtt 120 min plasma proinsulin (pm/l): 1.847572659,log10 bioimpedance: Resistance: 2.648360011,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 1.050420168,log10 serum bilirubin (umol/l): 1.51851394,log10 serum alanine aminotransfrase (u/l): 1.591064607,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.831869774,log10 ldl cholesterol (mmol/l): 0.663700925,log10 hdl cholesterol (mmol/l): 0.068185862,log10 total triglycerides (mmol/l): 0.359835482,log10 serum apoa1 (g/l): 0.176091259,log10 serum apob (g/l): 0.204119983,log10 urinary albumin excretion rate (ug/min): 1.021189299 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098359 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249258,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978186 | GSM1098359 | GSE45159 | 0.175422 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6835 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249258 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978186 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.359406774,log10 basal metabolic rate (kcal): 1701,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.466969775,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.685091663,plasma free fatty acids under the curve ogtt (mmol/l * min): 25.35,fat mass (%): 19.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.703903573,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 270,log10 homair (insulin resistance index based on homa): -0.318356824,log10 homais (insulin secretion index based on homa): 1.583576586,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.222586423,insgenin (insulinogenic index): 1.529150255,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.177218959,log10 matsuda insulin sensitivity index: 1.18991955,muscle mass (%): 46.3,lg10 serum c-reactive protein (mg/l): -0.375717904,lg10 plasma adiponectin (mg/l): 0.913813852,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 4.7,ogtt 30 min plasma glucose (mmol/l): 8,ogtt 120 min plasma glucose (mmol/l): 6.3,log10 il1 receptor antagonist (pg/ml): 2.114544267,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.361727836,ogtt 30 min plasma insulin (mu/l): 1.320146286,ogtt 120 min plasma insulin (mu/l): 1.521138084,log10 ogtt fasting plasma proinsulin (pm/l): 0.875061263,ogtt 30 min plasma proinsulin (pm/l): 1.340444115,ogtt 120 min plasma proinsulin (pm/l): 1.889861721,log10 bioimpedance: Resistance: 2.740362689,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 0.884615385,log10 serum bilirubin (umol/l): 1.397940009,log10 serum alanine aminotransfrase (u/l): 1.204119983,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.893206753,log10 ldl cholesterol (mmol/l): 0.701567985,log10 hdl cholesterol (mmol/l): 0.285557309,log10 total triglycerides (mmol/l): 0.195899652,log10 serum apoa1 (g/l): 0.264817823,log10 serum apob (g/l): 0.164352856,log10 urinary albumin excretion rate (ug/min): 0.927284796 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098360 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249259,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978187 | GSM1098360 | GSE45159 | 0.189403 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6849 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249259 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978187 |
|
1 | age: 49,tissue: adipose tissue,log10 body mass index: 1.438743981,log10 basal metabolic rate (kcal): 1875,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.607753084,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.080684217,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.8,fat mass (%): 20.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.719388821,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 147,log10 homair (insulin resistance index based on homa): 0.159433502,log10 homais (insulin secretion index based on homa): 1.687490187,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.679091597,insgenin (insulinogenic index): 2.1966641,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.640789409,log10 matsuda insulin sensitivity index: 0.756057086,muscle mass (%): 46.5,lg10 serum c-reactive protein (mg/l): 0.525951341,lg10 plasma adiponectin (mg/l): 0.995635195,ogtt fasting plasma free fatty acid (mmol/l): 0.22,ogtt 30 min plasma free fatty acid (mmol/l): 0.08,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 10.5,ogtt 120 min plasma glucose (mmol/l): 2.8,log10 il1 receptor antagonist (pg/ml): 2.088419617,log10 il1 beta (pg/ml): -0.823908741,log10 ogtt fasting plasma insulin (mu/l): 0.748188027,ogtt 30 min plasma insulin (mu/l): 2.109915863,ogtt 120 min plasma insulin (mu/l): 0.51851394,log10 ogtt fasting plasma proinsulin (pm/l): 1.133538908,ogtt 30 min plasma proinsulin (pm/l): 1.788168371,ogtt 120 min plasma proinsulin (pm/l): 1.340444115,log10 bioimpedance: Resistance: 2.622214023,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.980769231,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.62324929,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.852479994,log10 ldl cholesterol (mmol/l): 0.709269961,log10 hdl cholesterol (mmol/l): 0.1430148,log10 total triglycerides (mmol/l): 0.240549248,log10 serum apoa1 (g/l): 0.227886705,log10 serum apob (g/l): 0.212187604,log10 urinary albumin excretion rate (ug/min): 1.012234457 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098361 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249260,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978188 | GSM1098361 | GSE45159 | 0.329402 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6959 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249260 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978188 |
|
1 | age: 46,tissue: adipose tissue,log10 body mass index: 1.326356169,log10 basal metabolic rate (kcal): 1745,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.542995253,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.642833338,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.55,fat mass (%): 13.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.863411959,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 223.5,log10 homair (insulin resistance index based on homa): 0.108865574,log10 homais (insulin secretion index based on homa): 1.611014834,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.511027292,insgenin (insulinogenic index): 1.990848756,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.461018046,log10 matsuda insulin sensitivity index: 0.83759594,muscle mass (%): 51.4,lg10 serum c-reactive protein (mg/l): -0.853871964,lg10 plasma adiponectin (mg/l): 0.77815125,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 10.6,ogtt 120 min plasma glucose (mmol/l): 4.6,log10 il1 receptor antagonist (pg/ml): 2.042142183,log10 il1 beta (pg/ml): -0.853871964,log10 ogtt fasting plasma insulin (mu/l): 0.69019608,ogtt 30 min plasma insulin (mu/l): 1.911690159,ogtt 120 min plasma insulin (mu/l): 0.986771734,log10 ogtt fasting plasma proinsulin (pm/l): 0.968482949,ogtt 30 min plasma proinsulin (pm/l): 1.580924976,ogtt 120 min plasma proinsulin (pm/l): 1.505149978,log10 bioimpedance: Resistance: 2.698100546,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 0.894736842,log10 serum bilirubin (umol/l): 1.278753601,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.742725131,log10 ldl cholesterol (mmol/l): 0.42975228,log10 hdl cholesterol (mmol/l): 0.397940009,log10 total triglycerides (mmol/l): 0.004321374,log10 serum apoa1 (g/l): 0.318063335,log10 serum apob (g/l): -0.075720714,log10 urinary albumin excretion rate (ug/min): 0.84226875 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098362 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249261,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978189 | GSM1098362 | GSE45159 | 0.261834 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6969 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249261 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978189 |
|
1 | age: 49,tissue: adipose tissue,log10 body mass index: 1.426937881,log10 basal metabolic rate (kcal): 1889,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.425950451,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.96823083,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.45,fat mass (%): 21.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.942514505,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 264,log10 homair (insulin resistance index based on homa): 0.334453751,log10 homais (insulin secretion index based on homa): 1.811575006,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.615960567,insgenin (insulinogenic index): 1.934005495,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.549848944,log10 matsuda insulin sensitivity index: 0.635510293,muscle mass (%): 45.3,lg10 serum c-reactive protein (mg/l): 0.290257269,lg10 plasma adiponectin (mg/l): 0.740362689,ogtt fasting plasma free fatty acid (mmol/l): 0.29,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 10.1,ogtt 120 min plasma glucose (mmol/l): 6.4,log10 il1 receptor antagonist (pg/ml): 2.352568386,log10 il1 beta (pg/ml): -0.468521083,log10 ogtt fasting plasma insulin (mu/l): 0.908485019,ogtt 30 min plasma insulin (mu/l): 1.824776462,ogtt 120 min plasma insulin (mu/l): 1.786751422,log10 ogtt fasting plasma proinsulin (pm/l): 1.301029996,ogtt 30 min plasma proinsulin (pm/l): 1.480006943,ogtt 120 min plasma proinsulin (pm/l): 1.746634199,log10 bioimpedance: Resistance: 2.661812686,log10 bioimpedance (reactance): 1.69019608,waist to hip ratio: 0.961538462,log10 serum bilirubin (umol/l): 1.322219295,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.775974331,log10 ldl cholesterol (mmol/l): 0.625312451,log10 hdl cholesterol (mmol/l): 0.075546961,log10 total triglycerides (mmol/l): 0.136720567,log10 serum apoa1 (g/l): 0.1430148,log10 serum apob (g/l): 0.136720567,log10 urinary albumin excretion rate (ug/min): 1.045583738 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098363 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249262,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978190 | GSM1098363 | GSE45159 | 0.153173 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM6978 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249262 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978190 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.423580268,log10 basal metabolic rate (kcal): 1864,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.382194157,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.713048473,plasma free fatty acids under the curve ogtt (mmol/l * min): 7.95,fat mass (%): 18.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.395534135,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 1.5,log10 homair (insulin resistance index based on homa): 0.364488457,log10 homais (insulin secretion index based on homa): 1.947293649,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.626617488,insgenin (insulinogenic index): 2.76537048,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.551828011,log10 matsuda insulin sensitivity index: 0.702016197,muscle mass (%): 49.9,lg10 serum c-reactive protein (mg/l): 0.348304863,lg10 plasma adiponectin (mg/l): 0.568201724,ogtt fasting plasma free fatty acid (mmol/l): 0.13,ogtt 30 min plasma free fatty acid (mmol/l): 0.07,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 6.6,ogtt 120 min plasma glucose (mmol/l): 4.3,log10 il1 receptor antagonist (pg/ml): 2.130333768,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.968482949,ogtt 30 min plasma insulin (mu/l): 2.026941628,ogtt 120 min plasma insulin (mu/l): 1.071882007,log10 ogtt fasting plasma proinsulin (pm/l): 1.173186268,ogtt 30 min plasma proinsulin (pm/l): 1.669316881,ogtt 120 min plasma proinsulin (pm/l): 1.5289167,log10 bioimpedance: Resistance: 2.63447727,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 0.9375,log10 serum bilirubin (umol/l): 0.903089987,log10 serum alanine aminotransfrase (u/l): 1.505149978,log10 creatinine (umol/l): 1.949390007,log10 total cholesterol (mmol/l): 0.725094521,log10 ldl cholesterol (mmol/l): 0.51851394,log10 hdl cholesterol (mmol/l): 0.071882007,log10 total triglycerides (mmol/l): 0.23299611,log10 serum apoa1 (g/l): 0.1430148,log10 serum apob (g/l): 0.100370545,log10 urinary albumin excretion rate (ug/min): 0.748188027 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098364 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249263,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978191 | GSM1098364 | GSE45159 | 0.029699 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM7024 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249263 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978191 |
|
1 | age: 67,tissue: adipose tissue,log10 body mass index: 1.387324173,log10 basal metabolic rate (kcal): 1577,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.696284635,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.604518427,plasma free fatty acids under the curve ogtt (mmol/l * min): 8.1,fat mass (%): 23.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.0175044,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 256.5,log10 homair (insulin resistance index based on homa): 0.329962558,log10 homais (insulin secretion index based on homa): 1.693140461,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.524084409,insgenin (insulinogenic index): 1.631781873,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.448675408,log10 matsuda insulin sensitivity index: 0.655282359,muscle mass (%): 43.2,lg10 serum c-reactive protein (mg/l): 0.004321374,lg10 plasma adiponectin (mg/l): 1.064457989,ogtt fasting plasma free fatty acid (mmol/l): 0.16,ogtt 30 min plasma free fatty acid (mmol/l): 0.08,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 6.5,ogtt 30 min plasma glucose (mmol/l): 10.1,ogtt 120 min plasma glucose (mmol/l): 7.4,log10 il1 receptor antagonist (pg/ml): 1.976670881,log10 il1 beta (pg/ml): 0.045322979,log10 ogtt fasting plasma insulin (mu/l): 0.86923172,ogtt 30 min plasma insulin (mu/l): 1.519827994,ogtt 120 min plasma insulin (mu/l): 1.8876173,log10 ogtt fasting plasma proinsulin (pm/l): 1.1430148,ogtt 30 min plasma proinsulin (pm/l): 1.416640507,ogtt 120 min plasma proinsulin (pm/l): 1.895422546,log10 bioimpedance: Resistance: 2.656098202,log10 bioimpedance (reactance): 1.62324929,waist to hip ratio: 0.978723404,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.361727836,log10 creatinine (umol/l): 1.84509804,log10 total cholesterol (mmol/l): 0.767155866,log10 ldl cholesterol (mmol/l): 0.580924976,log10 hdl cholesterol (mmol/l): 0.161368002,log10 total triglycerides (mmol/l): 0.004321374,log10 serum apoa1 (g/l): 0.152288344,log10 serum apob (g/l): 0.017033339,log10 urinary albumin excretion rate (ug/min): 1.491361694 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098365 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249264,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978192 | GSM1098365 | GSE45159 | 0.216289 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM7080 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249264 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978192 |
|
1 | age: 62,tissue: adipose tissue,log10 body mass index: 1.443180789,log10 basal metabolic rate (kcal): 1652,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.141913953,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.344412393,plasma free fatty acids under the curve ogtt (mmol/l * min): 23.55,fat mass (%): 33.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.970824901,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 247.5,log10 homair (insulin resistance index based on homa): 0.232487866,log10 homais (insulin secretion index based on homa): 1.639201799,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.621228228,insgenin (insulinogenic index): 2.141275533,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.573022534,log10 matsuda insulin sensitivity index: 0.677050564,muscle mass (%): 45.9,lg10 serum c-reactive protein (mg/l): -0.102372909,lg10 plasma adiponectin (mg/l): 1.127104798,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.26,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.3,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 8.2,log10 il1 receptor antagonist (pg/ml): 2.281078841,log10 il1 beta (pg/ml): -0.823908741,log10 ogtt fasting plasma insulin (mu/l): 0.785329835,ogtt 30 min plasma insulin (mu/l): 1.835056102,ogtt 120 min plasma insulin (mu/l): 1.789580712,log10 ogtt fasting plasma proinsulin (pm/l): 1.245512668,ogtt 30 min plasma proinsulin (pm/l): 1.673941999,ogtt 120 min plasma proinsulin (pm/l): 1.897627091,log10 bioimpedance: Resistance: 2.696356389,log10 bioimpedance (reactance): 1.792391689,waist to hip ratio: 1.076923077,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.579783597,log10 creatinine (umol/l): 1.995635195,log10 total cholesterol (mmol/l): 0.793790385,log10 ldl cholesterol (mmol/l): 0.609594409,log10 hdl cholesterol (mmol/l): 0.240549248,log10 total triglycerides (mmol/l): -0.086186148,log10 serum apoa1 (g/l): 0.201397124,log10 serum apob (g/l): 0.025305865,log10 urinary albumin excretion rate (ug/min): 0.928395852 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098366 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249265,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978193 | GSM1098366 | GSE45159 | 0.255425 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM7343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249265 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978193 |
|
1 | age: 61,tissue: adipose tissue,log10 body mass index: 1.463195289,log10 basal metabolic rate (kcal): 1487,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.420219358,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.565064702,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.7,fat mass (%): 32.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.10656294,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 394.5,log10 homair (insulin resistance index based on homa): 0.734639839,log10 homais (insulin secretion index based on homa): 2.236789099,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.923285477,insgenin (insulinogenic index): 2.073133127,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.838244434,log10 matsuda insulin sensitivity index: 0.251851391,muscle mass (%): 42.3,lg10 serum c-reactive protein (mg/l): 0.922725458,lg10 plasma adiponectin (mg/l): 0.556302501,ogtt fasting plasma free fatty acid (mmol/l): 0.3,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 10.6,ogtt 120 min plasma glucose (mmol/l): 8.4,log10 il1 receptor antagonist (pg/ml): 2.390493527,log10 il1 beta (pg/ml): -0.408935393,log10 ogtt fasting plasma insulin (mu/l): 1.315970345,ogtt 30 min plasma insulin (mu/l): 2.054613055,ogtt 120 min plasma insulin (mu/l): 2.182699903,log10 ogtt fasting plasma proinsulin (pm/l): 1.418301291,ogtt 30 min plasma proinsulin (pm/l): 1.598790507,ogtt 120 min plasma proinsulin (pm/l): 1.883093359,log10 bioimpedance: Resistance: 2.664641976,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.971287129,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.579783597,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.685741739,log10 ldl cholesterol (mmol/l): 0.469822016,log10 hdl cholesterol (mmol/l): 0.008600172,log10 total triglycerides (mmol/l): 0.285557309,log10 serum apoa1 (g/l): 0.021189299,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 1.124282703 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098367 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249266,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978194 | GSM1098367 | GSE45159 | 0.267306 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM7421 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249266 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978194 |
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