cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8310551
title: Additional file 10: of Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

description: Table S7. Pairwise differences between methods for miRNA detection inconsistency estimates. Percent difference is calculated as the percent difference of the first method in the comparison relative to the second, thus Clontech had 61% more inconsistency than Illumina. Percent difference was calculated using more precise means than the rounded means shown in the table. Significant findings are highlighted in yellow. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.8310554
title: Additional file 11: of Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

description: Table S8. Pairwise differences between methods for number of isomiRs detected by each method. Percent difference is calculated as the percent difference of the first method in the comparison relative to the second, thus Clontech detected 41.39% more isomiRs than Illumina. Percent difference was calculated using more precise means than the rounded means shown in the table. Significant findings are highlighted in yellow. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.8310551.v1
title: Additional file 10: of Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

description: Table S7. Pairwise differences between methods for miRNA detection inconsistency estimates. Percent difference is calculated as the percent difference of the first method in the comparison relative to the second, thus Clontech had 61% more inconsistency than Illumina. Percent difference was calculated using more precise means than the rounded means shown in the table. Significant findings are highlighted in yellow. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.8310554.v1
title: Additional file 11: of Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

description: Table S8. Pairwise differences between methods for number of isomiRs detected by each method. Percent difference is calculated as the percent difference of the first method in the comparison relative to the second, thus Clontech detected 41.39% more isomiRs than Illumina. Percent difference was calculated using more precise means than the rounded means shown in the table. Significant findings are highlighted in yellow. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.8310476
title: Additional file 1: of Does long-term cadmium exposure influence the composition of pectic polysaccharides in the cell wall of Medicago sativa stems?

description: Quantitative LC-MS/MS data and protein assignments. Overview of the proteins that changed significantly in the different cell wall protein fractions. (XLSX 95 kb)
DOI: 10.6084/m9.figshare.8310476.v1
title: Additional file 1: of Does long-term cadmium exposure influence the composition of pectic polysaccharides in the cell wall of Medicago sativa stems?

description: Quantitative LC-MS/MS data and protein assignments. Overview of the proteins that changed significantly in the different cell wall protein fractions. (XLSX 95 kb)
DOI: 10.6084/m9.figshare.8310437
title: Additional file 6: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Potential cis targets of lncRNAs with GO term and KEGG pathway enrichment analysis. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8310440
title: Additional file 7: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Potential trans targets of lncRNAs with GO term and KEGG pathway enrichment analysis. (XLSX 28106 kb)
DOI: 10.6084/m9.figshare.8310437.v1
title: Additional file 6: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Potential cis targets of lncRNAs with GO term and KEGG pathway enrichment analysis. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8310440.v1
title: Additional file 7: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Potential trans targets of lncRNAs with GO term and KEGG pathway enrichment analysis. (XLSX 28106 kb)
DOI: 10.6084/m9.figshare.8310428
title: Additional file 5: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: GO term and KEGG pathway enrichment analysis of significant differentially expressed mRNAs in the three skin color groups. (XLSX 304 kb)
DOI: 10.6084/m9.figshare.8310422
title: Additional file 4: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Differentially expressed lncRNAs and mRNAs identified in the three different skin color groups. (XLSX 136 kb)
DOI: 10.6084/m9.figshare.8310428.v1
title: Additional file 5: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: GO term and KEGG pathway enrichment analysis of significant differentially expressed mRNAs in the three skin color groups. (XLSX 304 kb)
DOI: 10.6084/m9.figshare.8310422.v1
title: Additional file 4: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Differentially expressed lncRNAs and mRNAs identified in the three different skin color groups. (XLSX 136 kb)
DOI: 10.6084/m9.figshare.8310410
title: Additional file 3: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Known and novel lncRNAs identified in black, white and red skin samples from Koi carp. (XLSX 3809 kb)
DOI: 10.6084/m9.figshare.8310407
title: Additional file 2: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Quality control results of nine representative samples. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8310410.v1
title: Additional file 3: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Known and novel lncRNAs identified in black, white and red skin samples from Koi carp. (XLSX 3809 kb)
DOI: 10.6084/m9.figshare.8310407.v1
title: Additional file 2: of Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

description: Quality control results of nine representative samples. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8310341
title: Additional file 4: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

description: Data for persistence across our time series and sharing across subjects in an independent, large cohort for TCRβs in this study. The columns “aminoAcid”, ‘vGeneName”, “jGeneName”, and “tcr” are the same as for Additional file 3. The column “n_cmv_public” is the number of subjects (out of 778) that shared that TCRβ. The columns “num_occ_sub1_pbmc”, “num_occ_sub2_pbmc”, and “num_occ_sub3_pbmc” are the number of time points at which a given receptor was observed in the PBMC samples for Individual 01, 02, and 03, respectively. (TSV 60870 kb)
DOI: 10.6084/m9.figshare.8310341.v1
title: Additional file 4: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

description: Data for persistence across our time series and sharing across subjects in an independent, large cohort for TCRβs in this study. The columns “aminoAcid”, ‘vGeneName”, “jGeneName”, and “tcr” are the same as for Additional file 3. The column “n_cmv_public” is the number of subjects (out of 778) that shared that TCRβ. The columns “num_occ_sub1_pbmc”, “num_occ_sub2_pbmc”, and “num_occ_sub3_pbmc” are the number of time points at which a given receptor was observed in the PBMC samples for Individual 01, 02, and 03, respectively. (TSV 60870 kb)
DOI: 10.6084/m9.figshare.8310335
title: Additional file 3: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

description: Count, frequency, V, J, and CDR3 amino acid sequence data for high abundance TCRβs in each sample. This is a tab-delimited, gzip-compressed file. The column “tcr” corresponds to a label that identifies a unique combination of CDR3 amino acid sequence, V gene, and J gene observed in this study. The column “count (templates/reads)” represents the counts of a given receptor’s DNA sequence in the sequencing data. The column “frequencyCount (%)” is the relative abundance of that tcr within each sample, accounting for productive and nonproductive receptors. The columns “vGeneName” and “jGeneName are the IMGT assigned V and J genes. The column “aminoAcid” is the CDR3 amino acid sequence. (TSV 8820 kb)
DOI: 10.6084/m9.figshare.8310329
title: Additional file 2: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

description: Table S1. Overall TCRβ-sequencing statistics per sample: sequencing depth, productive TCRβ sequencing depth, fraction of productive TCRβ sequences, unique V genes identified, unique J genes identified, unique CDR3 sequences, unique TCRβs, unique TCRβ nucleotide sequences. Table S2. V gene usage across subject and T cell population, expressed as both a fraction of all unique productive TCRβs and as a mean total abundance per sample. Table S3. J gene usage across subject and T cell population, expressed as both a fraction of all unique productive TCRβs and as a mean total abundance per sample. Table S4. Sequence and abundance information for the largest cohort of closely correlated TCRβs identified in each individual by Spearman’s or Pearson’s correlation. Table S5. The fraction of TCRβs in each sample that occurred in 1–8 samples from that subject’s time series. Table S6. Mann-Whitney U test statistics for mean abundance of TCRβs occurring in different numbers of samples during the time series. Table S7. Mann-Whitney U test statistics for nucleotide redundancy of TCRβs occurring in different numbers of samples during the time series. Table S8. The fraction of TCRβs in each sample that were shared to different degrees among subjects in a large, independent cohort. (XLSX 80 kb)
DOI: 10.6084/m9.figshare.8310335.v1
title: Additional file 3: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

description: Count, frequency, V, J, and CDR3 amino acid sequence data for high abundance TCRβs in each sample. This is a tab-delimited, gzip-compressed file. The column “tcr” corresponds to a label that identifies a unique combination of CDR3 amino acid sequence, V gene, and J gene observed in this study. The column “count (templates/reads)” represents the counts of a given receptor’s DNA sequence in the sequencing data. The column “frequencyCount (%)” is the relative abundance of that tcr within each sample, accounting for productive and nonproductive receptors. The columns “vGeneName” and “jGeneName are the IMGT assigned V and J genes. The column “aminoAcid” is the CDR3 amino acid sequence. (TSV 8820 kb)
DOI: 10.6084/m9.figshare.8310329.v1
title: Additional file 2: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

description: Table S1. Overall TCRβ-sequencing statistics per sample: sequencing depth, productive TCRβ sequencing depth, fraction of productive TCRβ sequences, unique V genes identified, unique J genes identified, unique CDR3 sequences, unique TCRβs, unique TCRβ nucleotide sequences. Table S2. V gene usage across subject and T cell population, expressed as both a fraction of all unique productive TCRβs and as a mean total abundance per sample. Table S3. J gene usage across subject and T cell population, expressed as both a fraction of all unique productive TCRβs and as a mean total abundance per sample. Table S4. Sequence and abundance information for the largest cohort of closely correlated TCRβs identified in each individual by Spearman’s or Pearson’s correlation. Table S5. The fraction of TCRβs in each sample that occurred in 1–8 samples from that subject’s time series. Table S6. Mann-Whitney U test statistics for mean abundance of TCRβs occurring in different numbers of samples during the time series. Table S7. Mann-Whitney U test statistics for nucleotide redundancy of TCRβs occurring in different numbers of samples during the time series. Table S8. The fraction of TCRβs in each sample that were shared to different degrees among subjects in a large, independent cohort. (XLSX 80 kb)
DOI: 10.6084/m9.figshare.8310308
title: Additional file 2: of Offering mental health first aid to a person with depression: a Delphi study to re-develop the guidelines published in 2008

description: Results of Item Rating. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8310308.v1
title: Additional file 2: of Offering mental health first aid to a person with depression: a Delphi study to re-develop the guidelines published in 2008

description: Results of Item Rating. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8310209
title: MOESM1 of Laboratory tests with Lepidoptera to assess non-target effects of Bt maize pollen: analysis of current studies and recommendations for a standardised design

description: Additional file 1: Table S1. Overview and methodology of laboratory studies (tier1) submitted in EU market applications to test effects of Cry proteins on Lepidopteran larvae.
DOI: 10.6084/m9.figshare.8310209.v1
title: MOESM1 of Laboratory tests with Lepidoptera to assess non-target effects of Bt maize pollen: analysis of current studies and recommendations for a standardised design

description: Additional file 1: Table S1. Overview and methodology of laboratory studies (tier1) submitted in EU market applications to test effects of Cry proteins on Lepidopteran larvae.
DOI: 10.6084/m9.figshare.8310107
title: Additional file 1: of Reproductive toxicity of fluoroquinolones in birds

description: Table S1. Reproductive toxicity of fluoroquinolones in birds: supporting data. Measured data are given for 1. Chicken embryonic heart rate following exposure to fluoroquinolones (heartbeats per minute) and 2. Blood biochemistry parameters of birds hatching from enrofloxacin- and marbofloxacin-exposed eggs. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8309900
title: Physicochemical properties of the six tailing samples

description: This table presents the physicochemical properties of the six tailing samples
DOI: 10.6084/m9.figshare.8310107.v1
title: Additional file 1: of Reproductive toxicity of fluoroquinolones in birds

description: Table S1. Reproductive toxicity of fluoroquinolones in birds: supporting data. Measured data are given for 1. Chicken embryonic heart rate following exposure to fluoroquinolones (heartbeats per minute) and 2. Blood biochemistry parameters of birds hatching from enrofloxacin- and marbofloxacin-exposed eggs. (XLSX 19 kb)
DOI: 10.21942/uva.8309894
title: FOC NGS Clean data

description: FOC NGS Clean data
DOI: 10.21942/uva.8309894.v1
title: FOC NGS Clean data

description: FOC NGS Clean data
DOI: 10.6084/m9.figshare.8309873
title: Wing size data

description: Wing size data
DOI: 10.6084/m9.figshare.8309867
title: Fertility data

description: Fertility data
DOI: 10.6084/m9.figshare.8309864
title: Survival data

description: Fly and wasp survival data
DOI: 10.6084/m9.figshare.8309861
title: Wasp oviposition data

description: Wasp oviposition data
DOI: 10.6084/m9.figshare.8309873.v2
title: Wing size data

description: Wing size data
DOI: 10.6084/m9.figshare.8309867.v2
title: Fertility data

description: Fertility data
DOI: 10.6084/m9.figshare.8309873.v1
title: Wing size data

description: Wing size data
DOI: 10.6084/m9.figshare.8309861.v2
title: Wasp oviposition data

description: Wasp oviposition data
DOI: 10.6084/m9.figshare.8309861.v1
title: Wasp oviposition data

description: Wasp oviposition data
DOI: 10.6084/m9.figshare.8309867.v1
title: Fertility data

description: Fertility data
DOI: 10.6084/m9.figshare.8309864.v1
title: Survival data

description: Fly and wasp survival data
DOI: 10.6084/m9.figshare.8309822
title: Test-Table.jpg

description: Perfusion, oxygenation
DOI: 10.6084/m9.figshare.8309822.v1
title: Test-Table.jpg

description: Perfusion, oxygenation
DOI: 10.6084/m9.figshare.8309765
title: supplementary tables Zorz et al 2019 - resubmission.xlsx

description: Supplementary Tables associated with "A shared core microbiome in soda lakes separated by large distances" by Jackie K Zorz, Christine Sharp, Manuel Kleiner, Paul MK Gordon, Richard Pon, Xiaoli Dong, Marc Strous
DOI: 10.6084/m9.figshare.8309780
title: Supplementary Tables to Zorz et al 2019

description: Supplementary Tables associated with "A shared core microbiome in soda lakes separated by large distances" by Jackie K Zorz, Christine Sharp, Manuel Kleiner, Paul MK Gordon, Richard Pon, Xiaoli Dong, Marc Strous
DOI: 10.6084/m9.figshare.8309777
title: Greenland Ice Slabs Data

description: Zipfiles are sub-directories of data, to be downloaded and unzipped in a common directory.<br>Brief explanations of file structures are in the README.md file.<br><br>NOTE: Not all Regional Climate Model (RCM) source data is presented here. That data may be acquired by contacting the modeling groups (HIRHAM, MAR, RAMCO) and their associates who are co-authors on the paper.<br>For those interested, the file "Ice_Layer_Output_Thicknesses.csv" contains the track_name, lat, lon, and ice_thickness of each IceBridge trace where an ice slab was detected in IceBridge Accumulation Radar, 2010-2014. (Figure 2 in the paper.) This is the most-commonly-requested file, so if that's all you need, go there and you needn't bother downloading the rest.
DOI: 10.6084/m9.figshare.8309765.v1
title: supplementary tables Zorz et al 2019 - resubmission.xlsx

description: Supplementary Tables associated with "A shared core microbiome in soda lakes separated by large distances" by Jackie K Zorz, Christine Sharp, Manuel Kleiner, Paul MK Gordon, Richard Pon, Xiaoli Dong, Marc Strous
DOI: 10.6084/m9.figshare.8309780.v1
title: Supplementary Tables to Zorz et al 2019

description: Supplementary Tables associated with "A shared core microbiome in soda lakes separated by large distances" by Jackie K Zorz, Christine Sharp, Manuel Kleiner, Paul MK Gordon, Richard Pon, Xiaoli Dong, Marc Strous
DOI: 10.6084/m9.figshare.8309714
title: ECCITE-seq protein and mRNA counts

description: Protein data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3596101, file GSM3596101_CTCL-ADT-count.csv.gz.<br><code>velocyto</code> processing: velocyto run (bam directory)/(BAM file).bam (transcriptome directory)/genes/genes.gtf<br><br>
DOI: 10.6084/m9.figshare.8309708
title: REAP-seq protein and mRNA counts

description: Protein count data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2685243, file GSM2685243_protein_2_PBMCs_matrix.txt.gz, and processed into csv format.<br>Aligned bam file was acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2685238, file mRNA_2_PBMCs_possorted_genome_bam.bam.<br><code>velocyto</code> processing:<code>velocyto run (bam directory)/mRNA_2_PBMCs_possorted_genome_bam.bam(transcriptome directory)/genes/genes.gtf</code>
DOI: 10.6084/m9.figshare.8309696
title: CITE-seq protein and mRNA counts

description: Protein counts were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866. <br>LOOM was generated from FASTQ. <code>cellranger</code> processing:<code>cellranger count --id=(desired bam directory) --transcriptome=(transcriptome directory) --fastqs=(fastq directory) --localcores=40 --localmem=100 --chemistry=SC3Pv2</code><code>velocyto</code> processing: <code>velocyto run10x --samtools-threads 60 --samtools-memory 5000 (desired bam directory) (transcriptome directory)/genes/genes.gtf</code>
DOI: 10.6084/m9.figshare.8309681
title: Leukemia_157_extracted_features.txt

description: extracted features
DOI: 10.6084/m9.figshare.8309696.v1
title: CITE-seq protein and mRNA counts

description: Protein counts were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866. <br>LOOM was generated from FASTQ. <code>cellranger</code> processing:<code>cellranger count --id=(desired bam directory) --transcriptome=(transcriptome directory) --fastqs=(fastq directory) --localcores=40 --localmem=100 --chemistry=SC3Pv2</code><code>velocyto</code> processing: <code>velocyto run10x --samtools-threads 60 --samtools-memory 5000 (desired bam directory) (transcriptome directory)/genes/genes.gtf</code>
DOI: 10.6084/m9.figshare.8309681.v1
title: Leukemia_157_extracted_features.txt

description: extracted features
DOI: 10.6084/m9.figshare.8309660
title: Temporal induction of intestinal epithelial hypoxia-inducible factor (HIF)-2α is sufficient to drive colitis.

description: We used a new mouse model to evaluate the role of temporal induction of intestinal epithelial hypoxia-inducible factor (HIF)-2α in driving colitis.
DOI: 10.6084/m9.figshare.8309633
title: Data_JGR_space_physics

description: data for JGR space physics
DOI: 10.6084/m9.figshare.8309633.v1
title: Data_JGR_space_physics

description: data for JGR space physics
DOI: 10.6084/m9.figshare.8309660.v2
title: Temporal induction of intestinal epithelial hypoxia-inducible factor (HIF)-2α is sufficient to drive colitis.

description: We used a new mouse model to evaluate the role of temporal induction of intestinal epithelial hypoxia-inducible factor (HIF)-2α in driving colitis.
DOI: 10.6084/m9.figshare.8309660.v1
title: Temporal induction of intestinal epithelial hypoxia-inducible factor (HIF)-2α is sufficient to drive colitis.

description: We used a new mouse model to evaluate the role of temporal induction of intestinal epithelial hypoxia-inducible factor (HIF)-2α in driving colitis.
DOI: 10.6084/m9.figshare.8309567
title: Soil respiration dataset from a seasonally dry tropical forest

description: Dataset of soil CO<sub>2</sub> efflux from a seasonally dry tropical forest. Dataset includes information from January 2006 to April 2008. Soil CO2 efflux was measured using the "gradient method" where soil CO2 concentrations were measured in conjunction with soil temperature and soil moisture. The study site was hit by a hurricane on October 2005, thus soil CO2 efflux rates are high during the beginning of 2006. For more details about the study site and methodology please see:<br>Vargas, R., 2012. How a hurricane disturbance influences extreme CO2 fluxes and variance in a tropical forest. <i>Environmental Research Letters</i>, <i>7</i>(3), p.035704.<br> http://iopscience.iop.org/1748-9326/7/3/035704 <br>
DOI: 10.6084/m9.figshare.8309567.v2
title: Soil respiration dataset from a seasonally dry tropical forest

description: Dataset of soil CO<sub>2</sub> efflux from a seasonally dry tropical forest. Dataset includes information from January 2006 to April 2008. Soil CO2 efflux was measured using the "gradient method" where soil CO2 concentrations were measured in conjunction with soil temperature and soil moisture. The study site was hit by a hurricane on October 2005, thus soil CO2 efflux rates are high during the beginning of 2006. For more details about the study site and methodology please see:<br>Vargas, R., 2012. How a hurricane disturbance influences extreme CO2 fluxes and variance in a tropical forest. <i>Environmental Research Letters</i>, <i>7</i>(3), p.035704.<br> http://iopscience.iop.org/1748-9326/7/3/035704 <br>
DOI: 10.6084/m9.figshare.8309429
title: Responses from TurkPrime workers: Monitoring Twitter for clinical trial recruitment

description: This data set contains the results of a survey to examine the attitudes of TurkPrime users regarding the use of Twitter monitoring to enhance clinical trial recruitment. TurkPrime was used to recruit a representative panel of users to respond to the survey.