cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3770771_d4
title: Additional file 2: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 3239 significantly differentially methylated CpG sites between omental and abdominal subcutaneous adipose after weight loss. Illumina probe ID, gene name, gene region and chromosomal location (as Illumina 450K manifest) are shown along with methylation statistics. OM_mean_beta and AB_mean_beta present mean beta values for omental (OM) and abdominal subcutaneous (AB) adipose, respectively. We also indicate which CpG sites overlap with those observed in the post-weight loss analysis (Overlap_CpG), whether the change in methylation between SC and OM is greater at the post-weight loss time point (Greater_Î beta_Post) and whether the CpG site was observed as differentially methylation before vs after weight loss in AB (Overlap_AB_Benton_etal) and OM (Overlap_OM_Benton_etal) in our previous study [37]. (CSV 637 kb)
DOI: 10.6084/m9.figshare.c.3770771_d5.v1
title: Additional file 3: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 784 significant DMRs between omental and abdominal subcutaneous adipose before weight loss. Chromosomal location including DMR start and finish, number of CpG sites, gene symbol and level of differential methylation are included. (CSV 43 kb)
DOI: 10.6084/m9.figshare.c.3770771_d5
title: Additional file 3: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 784 significant DMRs between omental and abdominal subcutaneous adipose before weight loss. Chromosomal location including DMR start and finish, number of CpG sites, gene symbol and level of differential methylation are included. (CSV 43 kb)
DOI: 10.6084/m9.figshare.c.3770771_d6.v1
title: Additional file 4: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 1129 significant DMRs between omental and abdominal subcutaneous adipose after weight loss. Chromosomal location including DMR start and finish, number of CpG sites, gene symbol and level of differential methylation are included. (CSV 63 kb)
DOI: 10.6084/m9.figshare.c.3770771_d6
title: Additional file 4: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Annotated data for the 1129 significant DMRs between omental and abdominal subcutaneous adipose after weight loss. Chromosomal location including DMR start and finish, number of CpG sites, gene symbol and level of differential methylation are included. (CSV 63 kb)
DOI: 10.6084/m9.figshare.c.3770771_d7.v1
title: Additional file 5: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Enrichment results for genes mapping to DMRs only observed in the before weight loss analysis. All pathways passing Bonferroni correction (Pâ  â ¤â  0.05) are shown. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3770771_d7
title: Additional file 5: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Enrichment results for genes mapping to DMRs only observed in the before weight loss analysis. All pathways passing Bonferroni correction (Pâ  â ¤â  0.05) are shown. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3770813_d3
title: Additional file 3: of Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

description: Table listing all image-based distance measurements used for parameter inference. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.c.3770813_d4
title: Additional file 4: of Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

description: Entire set of measured distances between nine pairs of loci used to analyze distance distributions. (XLSX 160 kb)
DOI: 10.6084/m9.figshare.c.3770771_d11
title: Additional file 9: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Summary of Pearson’s correlation data passing a P ≤ 0.001 threshold for comparison of Δbeta (subcutaneous adipose vs omentum) and Δclinical trait (before vs after weight loss). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3770822_d4.v1
title: Additional file 4: of PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

description: Table S3. Differential expression results for calculated paternal-X expression between WT and Eed â  /â   TSCs. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.c.3770822_d3.v1
title: Additional file 3: of PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

description: Table S2. Paternal allele expression for X-chromosome genes withâ  â Ľâ  10x coverage at SNP sites. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.c.3770771_d10
title: Additional file 8: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Enrichment results for genes mapping to DMRs observed in both the before and after weight loss analyses, for which the methylation difference between tissues was greater after weight loss. All pathways passing Bonferroni correction (Pâ  â ¤â  0.05) are shown. (CSV 7 kb)
DOI: 10.6084/m9.figshare.c.3770771_d10.v1
title: Additional file 8: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

description: Enrichment results for genes mapping to DMRs observed in both the before and after weight loss analyses, for which the methylation difference between tissues was greater after weight loss. All pathways passing Bonferroni correction (Pâ  â ¤â  0.05) are shown. (CSV 7 kb)
DOI: 10.6084/m9.figshare.c.3770822_d3
title: Additional file 3: of PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

description: Table S2. Paternal allele expression for X-chromosome genes withâ  â Ľâ  10x coverage at SNP sites. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.c.3770813_d5.v1
title: Additional file 5: of Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

description: Mean square displacements measured on multiple chromatin loci in independent studies. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.c.3770834_d1.v1
title: MOESM1 of Determining economic productivity under environmental and resource pressures: an empirical application

description: Additional file 1. The dataset supporting the conclusions of this article is included within the article and its additional file. ( http://www.materialflows.net , http://stats.oecd.org/ , http://www.eia.gov/countries/data.cfm ).
DOI: 10.6084/m9.figshare.c.3770813_d5
title: Additional file 5: of Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

description: Mean square displacements measured on multiple chromatin loci in independent studies. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.c.3770834_d1
title: MOESM1 of Determining economic productivity under environmental and resource pressures: an empirical application

description: Additional file 1. The dataset supporting the conclusions of this article is included within the article and its additional file. ( http://www.materialflows.net , http://stats.oecd.org/ , http://www.eia.gov/countries/data.cfm ).
DOI: 10.6084/m9.figshare.c.3770822_d5.v1
title: Additional file 5: of PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

description: Table S4. Paternal allele expression for X-chromosome genes withâ  â Ľâ  5x coverage at SNP sites. (XLSX 113 kb)
DOI: 10.6084/m9.figshare.c.3770822_d4
title: Additional file 4: of PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

description: Table S3. Differential expression results for calculated paternal-X expression between WT and Eed â  /â   TSCs. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.c.3770822_d5
title: Additional file 5: of PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

description: Table S4. Paternal allele expression for X-chromosome genes withâ  â Ľâ  5x coverage at SNP sites. (XLSX 113 kb)
DOI: 10.6084/m9.figshare.c.3770813_d6.v1
title: Additional file 6: of Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

description: Zipped archive containing the scripts to run the best model simulation. (ZIP 241 kb)
DOI: 10.6084/m9.figshare.c.3770831_d2.v1
title: Additional file 2: Table S1. of Myocardial and haemodynamic responses to two fluid regimens in African children with severe malnutrition and hypovolaemic shock (AFRIM study)

description: a Clinical features (median, interquartile range and standard deviation) and prevalence (n; %) of abnormal signs at different time points in group 1 (bolus + rehydration). b Clinical features (median, interquartile range and standard deviation) and prevalence (n; %) of abnormal signs at different time points in group two (rehydration-only). (ZIP 55 kb)
DOI: 10.6084/m9.figshare.c.3770813_d6
title: Additional file 6: of Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

description: Zipped archive containing the scripts to run the best model simulation. (ZIP 241 kb)
DOI: 10.6084/m9.figshare.c.3772019_d1.v1
title: Additional file 1: Table S3. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

description: Phylogenomic relationships between our MAGs and a collection of 1758 reference genomes. (XLSX 775Â kb)
DOI: 10.6084/m9.figshare.c.3771989_d3
title: Additional file 3: Figure S1. of Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium

description: Jag-MM-silica plates with CMC and Congo red; Figure S2. Jag-MM-agar plates with starch. (ZIP 964Â kb)
DOI: 10.6084/m9.figshare.c.3772019_d1
title: Additional file 1: Table S3. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

description: Phylogenomic relationships between our MAGs and a collection of 1758 reference genomes. (XLSX 775Â kb)
DOI: 10.6084/m9.figshare.c.3772013_d1.v1
title: Additional file 1: of Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

description: Significant biological functions associated with the proliferative phase of adipogenesis determined by IPA software. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3772013_d1
title: Additional file 1: of Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

description: Significant biological functions associated with the proliferative phase of adipogenesis determined by IPA software. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3772019_d2.v1
title: Additional file 2: Table S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

description: Additional information for samples, metagenomic bins, and metagenome-assembled genomes in our study. (XLSX 180Â kb)
DOI: 10.6084/m9.figshare.c.3772019_d2
title: Additional file 2: Table S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

description: Additional information for samples, metagenomic bins, and metagenome-assembled genomes in our study. (XLSX 180Â kb)
DOI: 10.6084/m9.figshare.c.3772013_d2.v1
title: Additional file 2: of Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

description: List of genes from the highlighted biological functions associated with the proliferative phase of adipogenesis determined by IPA software. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.c.3772013_d2
title: Additional file 2: of Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

description: List of genes from the highlighted biological functions associated with the proliferative phase of adipogenesis determined by IPA software. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.c.3772022_d3.v1
title: Additional file 3: of European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

description: Homoplasies identified within C. abortus isolates. It should be noted that some of the homoplasies derived for the pmp genes may have resulted from mis-mapping. *This is not within the quinolone resistance-determining region of gyrA [44, 45] and is not thought to confer any resistant phenotype. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3772013_d4.v1
title: Additional file 4: of Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

description: List of genes from the highlighted biological functions associated with the differentiation phase of adipogenesis determined by IPA software. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.c.3772019_d6.v1
title: Additional file 6: Table S2. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

description: The canonical correspondence analysis (CCA) of 500 functions and 107 sub-systems. (XLSX 240 kb)
DOI: 10.6084/m9.figshare.c.3772016_d5.v1
title: Additional file 5: of Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

description: Heteroplasmic sites identified on the mitochondrial genomes of Loricarioidei catfishes. This spreadsheet file is sub-divided in 32 independent sheets; one containing the legend, another with a summary and one for each of the 31 Loricarioidei species, identified by their field numbers as detailed on TableÂ 2 in the main text. The sheets for each species show every heteroplasmic position identified, the total number of supporting reads, as well as, for each nucleotide, the absolute count and its proportion. On the Summary sheet, each column contains all the heteroplasmic positions found for a single species (identified on the column head). The first column on the left shows the gene where this position is located. Genes coding for ribosomal RNAs are colored in green, while genes coding for transfer RNAs are colored in blue and protein coding genes are colored in orange. Lines represent homologous positions among the mitochondrial genomes from the different species. Three conditions were used to characterize a heteroplasmic site: first, different nucleotides were sequenced in the same position; second, that position must have more than 100 supporting reads; and third, the frequency of the second most frequent base must be higher than 10%. On the Summary sheet, the positions with more than 1000 supporting reads are highlighted in red. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3772013_d4
title: Additional file 4: of Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

description: List of genes from the highlighted biological functions associated with the differentiation phase of adipogenesis determined by IPA software. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.c.3772019_d6
title: Additional file 6: Table S2. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

description: The canonical correspondence analysis (CCA) of 500 functions and 107 sub-systems. (XLSX 240 kb)
DOI: 10.6084/m9.figshare.c.3772022_d3
title: Additional file 3: of European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

description: Homoplasies identified within C. abortus isolates. It should be noted that some of the homoplasies derived for the pmp genes may have resulted from mis-mapping. *This is not within the quinolone resistance-determining region of gyrA [44, 45] and is not thought to confer any resistant phenotype. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3772016_d5
title: Additional file 5: of Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

description: Heteroplasmic sites identified on the mitochondrial genomes of Loricarioidei catfishes. This spreadsheet file is sub-divided in 32 independent sheets; one containing the legend, another with a summary and one for each of the 31 Loricarioidei species, identified by their field numbers as detailed on TableÂ 2 in the main text. The sheets for each species show every heteroplasmic position identified, the total number of supporting reads, as well as, for each nucleotide, the absolute count and its proportion. On the Summary sheet, each column contains all the heteroplasmic positions found for a single species (identified on the column head). The first column on the left shows the gene where this position is located. Genes coding for ribosomal RNAs are colored in green, while genes coding for transfer RNAs are colored in blue and protein coding genes are colored in orange. Lines represent homologous positions among the mitochondrial genomes from the different species. Three conditions were used to characterize a heteroplasmic site: first, different nucleotides were sequenced in the same position; second, that position must have more than 100 supporting reads; and third, the frequency of the second most frequent base must be higher than 10%. On the Summary sheet, the positions with more than 1000 supporting reads are highlighted in red. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3772022_d4.v1
title: Additional file 4: of European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

description: Pseudogenes identified within C. abortus isolates. Cells highlighted in brown indicate pseudogenes. * Pseudogene annotations have been refined from those published in Sait et al. 2011, according to the latest genome draft version. ** LLG annotation shows that this is a longer protein, CAB617-618, also disrupted. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3772022_d4
title: Additional file 4: of European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

description: Pseudogenes identified within C. abortus isolates. Cells highlighted in brown indicate pseudogenes. * Pseudogene annotations have been refined from those published in Sait et al. 2011, according to the latest genome draft version. ** LLG annotation shows that this is a longer protein, CAB617-618, also disrupted. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3772025_d2.v1
title: Additional file 4: of Codon 141 polymorphisms of the ovine prion protein gene affect the phenotype of classical scrapie transmitted from goats to sheep

description: clinical and pathological data. This file provides more detail about the clinical presentation, including scratch test score, and shows the individual PrPsc scores to create the brain PrPsc profiles as well as the scores for central nervous and lymphoid tissues obtained on the discriminatory IHC. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3772052_d1.v1
title: Additional file 1: Table S1. of 
                     RUNX2 repeat variation does not drive craniofacial diversity in marsupials

description: List of marsupial tissues and DNA samples used. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3772052_d1
title: Additional file 1: Table S1. of 
                     RUNX2 repeat variation does not drive craniofacial diversity in marsupials

description: List of marsupial tissues and DNA samples used. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3772052_d2.v1
title: Additional file 2: Table S2. of 
                     RUNX2 repeat variation does not drive craniofacial diversity in marsupials

description: Facial length measurement data. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3772061_d1
title: Additional file 1: of Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

description: shows descriptive data from deep sequencing of six samples including number of size filtered and adapter trimmed reads, and reads mapped as ssa-miRNAs in each sample. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3772052_d2
title: Additional file 2: Table S2. of 
                     RUNX2 repeat variation does not drive craniofacial diversity in marsupials

description: Facial length measurement data. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3772052_d3.v1
title: Additional file 3: Table S3. of 
                     RUNX2 repeat variation does not drive craniofacial diversity in marsupials

description: Repeat purity data. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3772052_d3
title: Additional file 3: Table S3. of 
                     RUNX2 repeat variation does not drive craniofacial diversity in marsupials

description: Repeat purity data. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3772061_d6
title: Additional file 6: of Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

description: shows complete results from target gene predictions using all Atlantic salmon transcripts in Refseq, Genbank as input in the in silico analysis (holistic approach). (XLSX 220 kb)
DOI: 10.6084/m9.figshare.c.3772061_d7.v1
title: Additional file 7: of Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

description: gives the consensus sequences of all promotor response elements included in the analysis of upstream miRNA gene sequences. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3772073_d1.v1
title: Additional file 1: of Rhinovirus C targets ciliated airway epithelial cells

description: C15-infected cells are shed from intact respiratory epithelium in vitro. HBEC-ALI cultures were infected for 18 h with C15 that expresses GFP during replication (C15-GFP, green) and fluorescently (Left, GFP video) or phase-contrast (Right, grayscale video) imaged every 10–15 min for 30 h. Notably shed cells are labeled in the first frame (black arrows). Original magnification: 20x. (ZIP 13284 kb)
DOI: 10.6084/m9.figshare.c.3772061_d7
title: Additional file 7: of Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

description: gives the consensus sequences of all promotor response elements included in the analysis of upstream miRNA gene sequences. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3772073_d1
title: Additional file 1: of Rhinovirus C targets ciliated airway epithelial cells

description: C15-infected cells are shed from intact respiratory epithelium in vitro. HBEC-ALI cultures were infected for 18 h with C15 that expresses GFP during replication (C15-GFP, green) and fluorescently (Left, GFP video) or phase-contrast (Right, grayscale video) imaged every 10–15 min for 30 h. Notably shed cells are labeled in the first frame (black arrows). Original magnification: 20x. (ZIP 13284 kb)
DOI: 10.6084/m9.figshare.c.3772112_d1.v1
title: Additional file 1: of A survey of proteomic biomarkers for heterotopic ossification in blood serum

description: Selection reaction monitoring (SRM) peptide transition parameters for protein candidates. Transition parameters and retention times of the 30 peptides were confirmed individually using an Agilent 6495 Triple Quadrapole Mass Spectrometer for both doubly and triply charged precursor ions. Five or 6 transitions per peptide precursor were selected for SRM analysis. In total, 350 transitions were optimized to identify and quantify 30 peptides. SRM target protein names, representative proteotypic peptide sequences, and SRM transition parameters are provided. (XLSX 68Â kb)