cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13346415.v1
title: Additional file 2 of DNA methylation of insulin-like growth factor 2 and H19 cluster in cord blood and prenatal air pollution exposure to fine particulate matter

description: Additional file 2. Supplementary Tables S1-S2.
DOI: 10.6084/m9.figshare.13346526
title: Additional file 10 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 10: File S4. Name of the RNA binding proteins with eCLIP data in K562.
DOI: 10.6084/m9.figshare.13346526.v1
title: Additional file 10 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 10: File S4. Name of the RNA binding proteins with eCLIP data in K562.
DOI: 10.6084/m9.figshare.13346529
title: Additional file 11 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 11: Table S6. Genomic overlap of circRNAs and RBP binding sites in HepG2 and K562.
DOI: 10.6084/m9.figshare.13346529.v1
title: Additional file 11 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 11: Table S6. Genomic overlap of circRNAs and RBP binding sites in HepG2 and K562.
DOI: 10.6084/m9.figshare.13346538
title: Additional file 14 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 14: Table S9. Primers for validating circRNA expression.
DOI: 10.6084/m9.figshare.13346538.v1
title: Additional file 14 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 14: Table S9. Primers for validating circRNA expression.
DOI: 10.6084/m9.figshare.13346535
title: Additional file 13 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 13: Table S8. GO enrichment analysis of RBPs that bind relatively more to BSJ circ-exons than non-circ-exons.
DOI: 10.6084/m9.figshare.13346535.v1
title: Additional file 13 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 13: Table S8. GO enrichment analysis of RBPs that bind relatively more to BSJ circ-exons than non-circ-exons.
DOI: 10.6084/m9.figshare.13346547
title: Additional file 2 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 2: File S2. Bash script containing the code to extract all K562 total RNA-Seq samples from ENCODE. The following samples were obtained for K562: total cell (n = 4), nucleus (n = 1), nucleoplasm (n = 1), nucleolus (n = 1), chromatin (n = 1), membrane (n = 1), cytosol (n = 1), and insoluble cytoplasmic fraction (n = 1).
DOI: 10.6084/m9.figshare.13346544.v1
title: Additional file 1 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 1: File S1. Bash script containing the code to extract all HepG2 total RNA-Seq samples from ENCODE. The following samples were obtained for HepG2: total cell (n = 1), nucleus (n = 1), membrane (n = 1), cytosol (n = 1), and insoluble cytoplasmic fraction (n = 1).
DOI: 10.6084/m9.figshare.13346547.v1
title: Additional file 2 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 2: File S2. Bash script containing the code to extract all K562 total RNA-Seq samples from ENCODE. The following samples were obtained for K562: total cell (n = 4), nucleus (n = 1), nucleoplasm (n = 1), nucleolus (n = 1), chromatin (n = 1), membrane (n = 1), cytosol (n = 1), and insoluble cytoplasmic fraction (n = 1).
DOI: 10.6084/m9.figshare.13346532.v1
title: Additional file 12 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 12: Table S7. Subcellular localization of RBPs in HepG2.
DOI: 10.6084/m9.figshare.13346544
title: Additional file 1 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 1: File S1. Bash script containing the code to extract all HepG2 total RNA-Seq samples from ENCODE. The following samples were obtained for HepG2: total cell (n = 1), nucleus (n = 1), membrane (n = 1), cytosol (n = 1), and insoluble cytoplasmic fraction (n = 1).
DOI: 10.6084/m9.figshare.13346559
title: Additional file 6 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 6: Table S4. Count matrix of backsplice junction reads supporting circRNAs in HepG2 txt).
DOI: 10.6084/m9.figshare.13346550.v1
title: Additional file 3 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 3: Table S1. Genomic and statistical information of the highly expressed circRNAs in K562 and HepG2. First six columns provide circRNA_ID, genomic positions of circRNAs, and information of circRNAs found in circBase. BSJ_reads and linear_reads give the number of reads supporting the circRNA and its corresponding linear transcript based on the CIRI2 pipeline. BSJ_reads_CIRCexplorer holds the number of reads supporting the circRNA by the CIRCexplorer pipeline. Exonic_length and N_exons hold the exonic length of the circRNA and the number of exons comprising the circRNA. N_RBPs give the number of RBPs with binding sites in the exonic part of the circRNA. RBP_overlap_bp is the number of bp overlapped by RBP binding sites (merged) in the exonic part of the circRNA. RBP_coverage is the fraction of the circRNA (exonic part) covered by RBP binding sites (RBP_overlap_bp/exonic_length*100). N_non_circ_exon_host_gene indicates the number of non-circularizing exons in the host gene. The mean RBP-coverage of non-circularizing exons in the host gene is provided in the column mean_RBP_coverage_non_circ_exons and was added a pseudo count of 1 to calculate the ratio between circRNA RBP-coverage and RBP-coverage of non-circ-exons in the host gene. This ratio is provided in Ratio_RBP_coverage_circRNA_non_circ_exons ((RBP_coverage+ 1)/(mean_RBP_coverage_non_circ_exons+ 1)).
DOI: 10.6084/m9.figshare.13346550
title: Additional file 3 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 3: Table S1. Genomic and statistical information of the highly expressed circRNAs in K562 and HepG2. First six columns provide circRNA_ID, genomic positions of circRNAs, and information of circRNAs found in circBase. BSJ_reads and linear_reads give the number of reads supporting the circRNA and its corresponding linear transcript based on the CIRI2 pipeline. BSJ_reads_CIRCexplorer holds the number of reads supporting the circRNA by the CIRCexplorer pipeline. Exonic_length and N_exons hold the exonic length of the circRNA and the number of exons comprising the circRNA. N_RBPs give the number of RBPs with binding sites in the exonic part of the circRNA. RBP_overlap_bp is the number of bp overlapped by RBP binding sites (merged) in the exonic part of the circRNA. RBP_coverage is the fraction of the circRNA (exonic part) covered by RBP binding sites (RBP_overlap_bp/exonic_length*100). N_non_circ_exon_host_gene indicates the number of non-circularizing exons in the host gene. The mean RBP-coverage of non-circularizing exons in the host gene is provided in the column mean_RBP_coverage_non_circ_exons and was added a pseudo count of 1 to calculate the ratio between circRNA RBP-coverage and RBP-coverage of non-circ-exons in the host gene. This ratio is provided in Ratio_RBP_coverage_circRNA_non_circ_exons ((RBP_coverage+ 1)/(mean_RBP_coverage_non_circ_exons+ 1)).
DOI: 10.6084/m9.figshare.13346553
title: Additional file 4 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 4: Table S2. Target sequences for siRNA-mediated knockdown of circCDYL, IGF2BP1, IGF2BP2, and GRWD1 in HepG2 and/or UMUC3 and J82.
DOI: 10.6084/m9.figshare.13346559.v1
title: Additional file 6 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 6: Table S4. Count matrix of backsplice junction reads supporting circRNAs in HepG2 txt).
DOI: 10.6084/m9.figshare.13346562
title: Additional file 7 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 7: Table S5. Count matrix of backsplice junction reads supporting circRNAs in K562.
DOI: 10.6084/m9.figshare.13346568.v1
title: Additional file 9 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 9: File S3. Name of the RNA binding proteins with eCLIP data in HepG2.
DOI: 10.6084/m9.figshare.13346556.v1
title: Additional file 5 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 5: Table S3. Sample information for HepG2 and K562.
DOI: 10.6084/m9.figshare.13346562.v1
title: Additional file 7 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 7: Table S5. Count matrix of backsplice junction reads supporting circRNAs in K562.
DOI: 10.6084/m9.figshare.13346556
title: Additional file 5 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 5: Table S3. Sample information for HepG2 and K562.
DOI: 10.6084/m9.figshare.13346691.v1
title: Additional file 4 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 4. Phylogenetic data matrices. Data matrix containing all scored taxa (38 taxa) and data matrix with all taxa used for final analysis (35 taxa).
DOI: 10.6084/m9.figshare.13346694
title: Additional file 5 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 5. Excel spreadsheet containing tables with summary statistics for all posterior parameter estimates, as well as divergence times and prior parameter values (effective priors) for important focal clades.
DOI: 10.6084/m9.figshare.13346694.v1
title: Additional file 5 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 5. Excel spreadsheet containing tables with summary statistics for all posterior parameter estimates, as well as divergence times and prior parameter values (effective priors) for important focal clades.
DOI: 10.6084/m9.figshare.13346680
title: Additional file 1 of Influence of APOE genotype in primary age-related tauopathy

description: Additional file 1 .Table 1. Neuropathological overview of the 152 eligible participants. Description of data: Breakdown of neuropathological findings which was used to determine pathology groups for the present study. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.13346680.v1
title: Additional file 1 of Influence of APOE genotype in primary age-related tauopathy

description: Additional file 1 .Table 1. Neuropathological overview of the 152 eligible participants. Description of data: Breakdown of neuropathological findings which was used to determine pathology groups for the present study. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.13346691
title: Additional file 4 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 4. Phylogenetic data matrices. Data matrix containing all scored taxa (38 taxa) and data matrix with all taxa used for final analysis (35 taxa).
DOI: 10.6084/m9.figshare.13346697.v1
title: Additional file 6 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 6. Input files including the dataset and all necessary coding (see Mr. Bayes blocks) to reproduce the analyses.
DOI: 10.6084/m9.figshare.13346700
title: Additional file 7 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 7. R scripts used for the construction of the main text figures and statistical analyses.
DOI: 10.6084/m9.figshare.13346697
title: Additional file 6 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 6. Input files including the dataset and all necessary coding (see Mr. Bayes blocks) to reproduce the analyses.
DOI: 10.6084/m9.figshare.13346700.v1
title: Additional file 7 of Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

description: Additional file 7. R scripts used for the construction of the main text figures and statistical analyses.
DOI: 10.6084/m9.figshare.13346725.v1
title: Additional file 1 of Alternative splicing in endothelial cells: novel therapeutic opportunities in cancer angiogenesis

description: Additional file 1: Supplementary Table 1. Additional AS isoforms (or events) relevant for angiogenesis and EC biology. Supplementary Table 2. RBPs whose deficiency results in aberrant vascular phenotypes in mice (MGI database) or Zebrafish (Danio rerio) (ZFIN database).
DOI: 10.6084/m9.figshare.13346725
title: Additional file 1 of Alternative splicing in endothelial cells: novel therapeutic opportunities in cancer angiogenesis

description: Additional file 1: Supplementary Table 1. Additional AS isoforms (or events) relevant for angiogenesis and EC biology. Supplementary Table 2. RBPs whose deficiency results in aberrant vascular phenotypes in mice (MGI database) or Zebrafish (Danio rerio) (ZFIN database).
DOI: 10.6084/m9.figshare.13346817
title: Additional file 1 of Plasma lipidome abnormalities in people with HIV initiating antiretroviral therapy

description: Additional file 1: Table 1. Lipid species concentrations. Plasma samples were thawed and the concentrations (μM) of the most abundant lipid metabolites (~1300) from 14 different lipid classes were measured by Complex Lipid Panel (Metabolon). Mean levels are reported. Statistical significance between study groups with and without HIV was determined using 2-sample unpaired t tests, and among samples from PWH at baseline and after 48 weeks of ART, paired t testing was used. P&lt;0.05 was used for significance cutoff, and significant values are shown in bold.
DOI: 10.6084/m9.figshare.13346820
title: Additional file 2 of Plasma lipidome abnormalities in people with HIV initiating antiretroviral therapy

description: Additional file 2: Table 2. Lipid species composition. Plasma samples were thawed and the proportional representation (mol%) among the most abundant lipid metabolites (~1300) from 14 different lipid classes were measured by Complex Lipid Panel (Metabolon). Mean levels are reported. Statistical significance between study groups with and without HIV was determined using 2-sample unpaired t tests, and among samples from PWH at baseline and after 48 weeks of ART, paired t testing was used. P&lt;0.05 was used for significance cutoff, and significant values are shown in bold.
DOI: 10.6084/m9.figshare.13346817.v1
title: Additional file 1 of Plasma lipidome abnormalities in people with HIV initiating antiretroviral therapy

description: Additional file 1: Table 1. Lipid species concentrations. Plasma samples were thawed and the concentrations (μM) of the most abundant lipid metabolites (~1300) from 14 different lipid classes were measured by Complex Lipid Panel (Metabolon). Mean levels are reported. Statistical significance between study groups with and without HIV was determined using 2-sample unpaired t tests, and among samples from PWH at baseline and after 48 weeks of ART, paired t testing was used. P&lt;0.05 was used for significance cutoff, and significant values are shown in bold.
DOI: 10.6084/m9.figshare.13346820.v1
title: Additional file 2 of Plasma lipidome abnormalities in people with HIV initiating antiretroviral therapy

description: Additional file 2: Table 2. Lipid species composition. Plasma samples were thawed and the proportional representation (mol%) among the most abundant lipid metabolites (~1300) from 14 different lipid classes were measured by Complex Lipid Panel (Metabolon). Mean levels are reported. Statistical significance between study groups with and without HIV was determined using 2-sample unpaired t tests, and among samples from PWH at baseline and after 48 weeks of ART, paired t testing was used. P&lt;0.05 was used for significance cutoff, and significant values are shown in bold.
DOI: 10.6084/m9.figshare.13346827
title: Additional file 1 of Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

description: Additional file 1: Table S1. Linkage map constructed using ASMap with corrected and imputed ddRAD markers derived from an BnSOSR x BnWOSR F2 population. Table S2. Mean markers and linkage map sizes across maps generated in this study. Abbreviations: doubled haploid (DH), recombinant inbred lines (RIL), amplified fragment length polymorphisms (AFLP), Brassica 60 K genotyping array (Brassica 60 k). Table S3. Phenotypic variation in flowering time and time to bud in the F2 mapping population and the parental lines. Phenotypes of spring type BnSOSR and winter type BnWOSR parental lines are shown as means of all replicates of each type (n = 4, n = 3, respectively). Table S4. QTL identified using genome-wide single QTL scans for budding time (B) and flowering time (FT). For each QTL, the phenotypic variance explained (PVE) and additive effect (AE) are shown. Table S5. Summary of variants impacting candidate flowering time genes on chromosome C2. The QTL regions ranges from 4,345,729 to 24,916,709. Table S6. Exon coverage of candidate genes on chromosome 2 generated by whole genome skim sequencing of 16 early-flowering and 19 late-flowering F2 individuals. Table S7. Summary of intergenic variants impacting candidate genes and segregating between early-flowering and late-flowering F2 individuals. Table S8. In silico double enzyme digest analysis. Frag: Total number of fragments; FragDe: total number of different end fragments; LengthDeFrag: total length in bases of different end fragments; DeFrag100–600: total number of different end fragments between 100 bases and 600 bases; LengthDeFrag100–600: total length in bases of different end fragments between 100 bases and 600 bases; % Coverage: percentage of the reference genome covered by fragments between 100 bases and 600 bases. Table S9. Phenotype data for flowering time and budding time in the mapping population and parents. Table S10. Sample list for the 194 progeny and 7 parental individuals used in this study.
DOI: 10.6084/m9.figshare.13203469
title: Additional file 2 of Spontaneous regression of micro-metastases following primary tumor excision: a critical role for primary tumor secretome

description: Additional file 2: Table S2. Extracellular proteins within the identified MDA-MB-231HM secretome. Table S3. Identified proteins in MDA-MB-231HM conditioned medium.
DOI: 10.6084/m9.figshare.13203469.v1
title: Additional file 2 of Spontaneous regression of micro-metastases following primary tumor excision: a critical role for primary tumor secretome

description: Additional file 2: Table S2. Extracellular proteins within the identified MDA-MB-231HM secretome. Table S3. Identified proteins in MDA-MB-231HM conditioned medium.
DOI: 10.6084/m9.figshare.13346904
title: Additional file 1 of Efficacy and safety of atropine to control myopia progression: a systematic review and meta-analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.13346904.v1
title: Additional file 1 of Efficacy and safety of atropine to control myopia progression: a systematic review and meta-analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.13346976
title: Additional file 1 of Distinct mutation profiles between primary bladder cancer and circulating tumor cells warrant the use of circulating tumors cells as cellular resource for mutation follow-up

description: Additional file 1.
DOI: 10.6084/m9.figshare.13346976.v1
title: Additional file 1 of Distinct mutation profiles between primary bladder cancer and circulating tumor cells warrant the use of circulating tumors cells as cellular resource for mutation follow-up

description: Additional file 1.
DOI: 10.6084/m9.figshare.13346979
title: Additional file 2 of Distinct mutation profiles between primary bladder cancer and circulating tumor cells warrant the use of circulating tumors cells as cellular resource for mutation follow-up

description: Additional file 2.
DOI: 10.6084/m9.figshare.13346979.v1
title: Additional file 2 of Distinct mutation profiles between primary bladder cancer and circulating tumor cells warrant the use of circulating tumors cells as cellular resource for mutation follow-up

description: Additional file 2.
DOI: 10.6084/m9.figshare.13346980
title: Additional file 1 of Immune-related protein signature in serum stratify relapsed mantle cell lymphoma patients based on risk

description: Additional file 1 Supplementary Table 1. Antibody clones used in the microarray platform targeting a total of 158 unique antigens.
DOI: 10.6084/m9.figshare.13346980.v1
title: Additional file 1 of Immune-related protein signature in serum stratify relapsed mantle cell lymphoma patients based on risk

description: Additional file 1 Supplementary Table 1. Antibody clones used in the microarray platform targeting a total of 158 unique antigens.
DOI: 10.6084/m9.figshare.13346541
title: Additional file 15 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 15: Table S10. qPCR primers to detect circCDYL and CDYL host gene expression levels.
DOI: 10.6084/m9.figshare.13346541.v1
title: Additional file 15 of Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

description: Additional file 15: Table S10. qPCR primers to detect circCDYL and CDYL host gene expression levels.