cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19321042
title: Additional file 1 of The microbiome of common bedding materials before and after use on commercial dairy farms

description: Additional file 1: Table S1. Metadata file for all samples included in this study. Table S2. ASVs assigned to each taxonomic level. Table S3. Read counts and mean abundance of assigned species stratified by sample ID. Table S4. Proportion of phylum-level counts, by bedding type and status. Table S5. Proportion of phylum-level counts, for the four non-outlier low-yielding bedding samples. Table S6. Modeling results for associations between bedding status and type, and alpha diversity metrics (LMM output). Table S7. Results from phylum-level differential abundance testing of used versus unused samples, by bedding type. Table S8. Results from class-level differential abundance testing of used versus unused samples, by bedding type. Table S9. Results from genus-level differential abundance testing of used versus unused samples, by bedding type. Table S10. List of potential mastitis pathogens considered in the analysis of 16S rRNA sequence data. Table S11. Proportion of genus-level counts for genera that contain potential mastitis pathogens, by bedding type and status. Table S12. Results from genus-level differential abundance testing of taxa that contain potential mastitis pathogens, comparing used versus unused samples, by bedding type. Table S13. Read counts and proportion of genus-level counts for the mock community and negative control samples.
DOI: 10.6084/m9.figshare.19321138
title: Additional file 2 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 2: Supplementary Table S1. Somatic Cell Count in milk during the animal trial.
DOI: 10.6084/m9.figshare.19321138.v1
title: Additional file 2 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 2: Supplementary Table S1. Somatic Cell Count in milk during the animal trial.
DOI: 10.6084/m9.figshare.19321144
title: Additional file 4 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 4: Supplementary Table S3. Sequencing output smallRNA-seq.
DOI: 10.6084/m9.figshare.19321144.v1
title: Additional file 4 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 4: Supplementary Table S3. Sequencing output smallRNA-seq.
DOI: 10.6084/m9.figshare.19321147
title: Additional file 5 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 5: Supplementary Table S4. All miRNAs found in milk EV samples.
DOI: 10.6084/m9.figshare.19321147.v1
title: Additional file 5 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 5: Supplementary Table S4. All miRNAs found in milk EV samples.
DOI: 10.6084/m9.figshare.19321156
title: Additional file 8 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 8: Supplementary Table S7. miRNA-target enrichment and network analysis of upregulated miRNAs.
DOI: 10.6084/m9.figshare.19321156.v1
title: Additional file 8 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 8: Supplementary Table S7. miRNA-target enrichment and network analysis of upregulated miRNAs.
DOI: 10.6084/m9.figshare.19321159.v1
title: Additional file 9 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 9: Supplementary Table S8. miRNA-target enrichment and network analysis of downregulated miRNAs.
DOI: 10.6084/m9.figshare.19321159
title: Additional file 9 of Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis

description: Additional file 9: Supplementary Table S8. miRNA-target enrichment and network analysis of downregulated miRNAs.
DOI: 10.6084/m9.figshare.19321160
title: Additional file 1 of Cultural adaptation of the mental health first aid guidelines for Brazilians with problem drinking: a Delphi expert consensus study

description: Additional file 1. Statements that were presented to the panels and their ratings across 3 rounds of the survey.
DOI: 10.6084/m9.figshare.19321160.v1
title: Additional file 1 of Cultural adaptation of the mental health first aid guidelines for Brazilians with problem drinking: a Delphi expert consensus study

description: Additional file 1. Statements that were presented to the panels and their ratings across 3 rounds of the survey.
DOI: 10.6084/m9.figshare.19321196
title: Additional file 1 of Transcriptomic characterization of the molecular mechanisms induced by RGMa during skeletal muscle nuclei accretion and hypertrophy

description: Additional file1: Supplementary file 1. Differentially expressed transcripts modulated by RGMa treatment during the differentiation of C2C12 cells.
DOI: 10.6084/m9.figshare.19321199
title: Additional file 2 of Transcriptomic characterization of the molecular mechanisms induced by RGMa during skeletal muscle nuclei accretion and hypertrophy

description: Additional file 2: Supplementary file 2. Differentially expressed genes modulated by RGMa treatment during the differentiation of C2C12 cell.
DOI: 10.6084/m9.figshare.19321196.v1
title: Additional file 1 of Transcriptomic characterization of the molecular mechanisms induced by RGMa during skeletal muscle nuclei accretion and hypertrophy

description: Additional file1: Supplementary file 1. Differentially expressed transcripts modulated by RGMa treatment during the differentiation of C2C12 cells.
DOI: 10.6084/m9.figshare.19321199.v1
title: Additional file 2 of Transcriptomic characterization of the molecular mechanisms induced by RGMa during skeletal muscle nuclei accretion and hypertrophy

description: Additional file 2: Supplementary file 2. Differentially expressed genes modulated by RGMa treatment during the differentiation of C2C12 cell.
DOI: 10.6084/m9.figshare.19321220
title: Additional file 2 of Single-cell transcriptomics of popliteal lymphatic vessels and peripheral veins reveals altered lymphatic muscle and immune cell populations in the TNF-Tg arthritis model

description: Additional file 2.
DOI: 10.6084/m9.figshare.19321220.v1
title: Additional file 2 of Single-cell transcriptomics of popliteal lymphatic vessels and peripheral veins reveals altered lymphatic muscle and immune cell populations in the TNF-Tg arthritis model

description: Additional file 2.
DOI: 10.6084/m9.figshare.19321216
title: Additional file 2 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 2: Table S2. The upstream and downstream transposable elements of MBD genes.
DOI: 10.6084/m9.figshare.19321213
title: Additional file 1 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 1: Table S1. The five duplicated types of MBD genes in B. napus and its ancestors.
DOI: 10.6084/m9.figshare.19321213.v1
title: Additional file 1 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 1: Table S1. The five duplicated types of MBD genes in B. napus and its ancestors.
DOI: 10.6084/m9.figshare.19321222
title: Additional file 4 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 4: Table S3. MBD family member characteristics and subcellular localization.
DOI: 10.6084/m9.figshare.19321216.v1
title: Additional file 2 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 2: Table S2. The upstream and downstream transposable elements of MBD genes.
DOI: 10.6084/m9.figshare.19321222.v1
title: Additional file 4 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 4: Table S3. MBD family member characteristics and subcellular localization.
DOI: 10.6084/m9.figshare.19321231
title: Additional file 7 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 7: Table S6. The |log2FC| of MBD genes in four tissues.
DOI: 10.6084/m9.figshare.19321231.v1
title: Additional file 7 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 7: Table S6. The |log2FC| of MBD genes in four tissues.
DOI: 10.6084/m9.figshare.19321225
title: Additional file 5 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 5: Table S4. Synteny analysis of MBD genes in B. rapa, B. oleracea, B. napus and A. thaliana.
DOI: 10.6084/m9.figshare.19321225.v1
title: Additional file 5 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 5: Table S4. Synteny analysis of MBD genes in B. rapa, B. oleracea, B. napus and A. thaliana.
DOI: 10.6084/m9.figshare.19321228
title: Additional file 6 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 6: Table S5. FPKM values of MBD genes in B. rapa, B. oleracea and B. napus.
DOI: 10.6084/m9.figshare.19321228.v1
title: Additional file 6 of The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

description: Additional file 6: Table S5. FPKM values of MBD genes in B. rapa, B. oleracea and B. napus.
DOI: 10.6084/m9.figshare.19321232.v1
title: Additional file 1 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 1: Table S1. Sequence read archive accession numbers for the sequenced animals. The spreadsheet file contains accession numbers from the European Nucleotide Archive that point to sequencing data for cattle from various breeds. The data in the file are organized in three spreadsheets. The accession for the bull that produced ejaculates with poor quality is listed in «case_SRA_ID». Accessions for 397 fertile control animals from various breeds are listed in «controls_SRA_IDs». Accessions, sequence-based genotypes and haplotypes for 285 cattle used to assign the 1-bp deletion onto a haplotype are listed in «array-based genotypes».
DOI: 10.6084/m9.figshare.19321238
title: Additional file 3 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 3: Table S3. Accessions for the eQTL cohort. Accessions for sequencing reads obtained from RNA and DNA prepared from testis tissue of 76 mature bulls.
DOI: 10.6084/m9.figshare.19321238.v1
title: Additional file 3 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 3: Table S3. Accessions for the eQTL cohort. Accessions for sequencing reads obtained from RNA and DNA prepared from testis tissue of 76 mature bulls.
DOI: 10.6084/m9.figshare.19321232
title: Additional file 1 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 1: Table S1. Sequence read archive accession numbers for the sequenced animals. The spreadsheet file contains accession numbers from the European Nucleotide Archive that point to sequencing data for cattle from various breeds. The data in the file are organized in three spreadsheets. The accession for the bull that produced ejaculates with poor quality is listed in «case_SRA_ID». Accessions for 397 fertile control animals from various breeds are listed in «controls_SRA_IDs». Accessions, sequence-based genotypes and haplotypes for 285 cattle used to assign the 1-bp deletion onto a haplotype are listed in «array-based genotypes».
DOI: 10.6084/m9.figshare.19321241.v1
title: Additional file 4 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 4: Table S4. Candidate causal variants. Functional consequences predicted for 1655 variants that are compatible with recessive inheritance based on the Ensembl (version 104) and Refseq (version 106) annotation of the bovine genome.
DOI: 10.6084/m9.figshare.19321235
title: Additional file 2 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 2: Table S2. Coordinates of a diagnostic haplotype. Illumina BovineHD coordinates (SNP-name, chromosome, physical position [ARS-UCD1.2]) and haplotype allele of 181 markers that define the diagnostic 675-kb haplotype.
DOI: 10.6084/m9.figshare.19321235.v1
title: Additional file 2 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 2: Table S2. Coordinates of a diagnostic haplotype. Illumina BovineHD coordinates (SNP-name, chromosome, physical position [ARS-UCD1.2]) and haplotype allele of 181 markers that define the diagnostic 675-kb haplotype.
DOI: 10.6084/m9.figshare.19321241
title: Additional file 4 of A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

description: Additional file 4: Table S4. Candidate causal variants. Functional consequences predicted for 1655 variants that are compatible with recessive inheritance based on the Ensembl (version 104) and Refseq (version 106) annotation of the bovine genome.
DOI: 10.6084/m9.figshare.19321274
title: Additional file 2 of StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

description: Additional file 2. Identifiers of genomes in the Escherichia and Enterococcus StrainGST reference databases.
DOI: 10.6084/m9.figshare.19321277
title: Additional file 3 of StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

description: Additional file 3. Identifiers of clinical gut microbiome datasets.
DOI: 10.6084/m9.figshare.19321274.v1
title: Additional file 2 of StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

description: Additional file 2. Identifiers of genomes in the Escherichia and Enterococcus StrainGST reference databases.
DOI: 10.6084/m9.figshare.19321277.v1
title: Additional file 3 of StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

description: Additional file 3. Identifiers of clinical gut microbiome datasets.
DOI: 10.6084/m9.figshare.19321304.v1
title: Additional file 2 of Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

description: Additional file 2. The age contribution, in years, for each of the 353 CpG sites comprising Horvath's clock, for each of the 1441 individuals.
DOI: 10.6084/m9.figshare.19321304
title: Additional file 2 of Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

description: Additional file 2. The age contribution, in years, for each of the 353 CpG sites comprising Horvath's clock, for each of the 1441 individuals.
DOI: 10.6084/m9.figshare.19321307
title: Additional file 3 of Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

description: Additional file 3. The SD and the rank by SD of the most variable CpG sites from Horvath's clock in three different populations: Men, Woman, and gender mixed population.
DOI: 10.6084/m9.figshare.19321307.v1
title: Additional file 3 of Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

description: Additional file 3. The SD and the rank by SD of the most variable CpG sites from Horvath's clock in three different populations: Men, Woman, and gender mixed population.
DOI: 10.6084/m9.figshare.19321313
title: Additional file 4 of Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

description: Additional file 4. The correlation between the methylation of the CpG site included in Horvath clock and other CpG sites related to the same gene, as a function of their distance, for the nine selected most variable genes found in all age groups.
DOI: 10.6084/m9.figshare.19321313.v1
title: Additional file 4 of Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

description: Additional file 4. The correlation between the methylation of the CpG site included in Horvath clock and other CpG sites related to the same gene, as a function of their distance, for the nine selected most variable genes found in all age groups.
DOI: 10.6084/m9.figshare.19321336
title: Additional file 1 of Evaluating a multi-component intervention to reduce and break up office workers’ sitting with sit-stand desks using the APEASE criteria

description: Additional file 1. Table that shows the completed COREQ checklist.xlsx.
DOI: 10.6084/m9.figshare.19321379
title: Additional file 3 of Immunogenetic variation shapes the gut microbiome in a natural vertebrate population

description: Additional file 2. The identity of 19 amplicon sequencing variants (ASVs) identified in the negative extraction controls. A taxonomic breakdown and the number of reads associated with each ASV is provided. ASVs were either filtered from the dataset before further analysis or retained. In the second tab is a detailed breakdown of number of reads with each ASV present in each sample, along with whether it is a negative control or faecal sample, and whether it was sequenced in the 1st, 2nd, or 3rd sequencing run.
DOI: 10.6084/m9.figshare.19321379.v1
title: Additional file 3 of Immunogenetic variation shapes the gut microbiome in a natural vertebrate population

description: Additional file 2. The identity of 19 amplicon sequencing variants (ASVs) identified in the negative extraction controls. A taxonomic breakdown and the number of reads associated with each ASV is provided. ASVs were either filtered from the dataset before further analysis or retained. In the second tab is a detailed breakdown of number of reads with each ASV present in each sample, along with whether it is a negative control or faecal sample, and whether it was sequenced in the 1st, 2nd, or 3rd sequencing run.
DOI: 10.6084/m9.figshare.19321382.v1
title: Additional file 4 of Immunogenetic variation shapes the gut microbiome in a natural vertebrate population

description: Additional file 3. Differentially abundant ASVs (Padj &lt; 0.01) in the gut microbiomes of Seychelles warblers, according to the presence/absence of the MHC-I alleles A) Ase-ua7 B) Ase-ua11 or C) Ase-ua1/10. Differential ASV abundance was assessed using negative binomial Wald tests and P values were adjusted using the Benjamini and Hochberg false-discovery rate correction with a significance cut-off of P &lt; 0.01. ASVs shown with a log2-fold change greater than zero are significantly more abundant in individuals without this allele and ASVs with a log2 fold change smaller than zero are significantly more abundant in individuals with a copy of this allele.
DOI: 10.6084/m9.figshare.19321382
title: Additional file 4 of Immunogenetic variation shapes the gut microbiome in a natural vertebrate population

description: Additional file 3. Differentially abundant ASVs (Padj &lt; 0.01) in the gut microbiomes of Seychelles warblers, according to the presence/absence of the MHC-I alleles A) Ase-ua7 B) Ase-ua11 or C) Ase-ua1/10. Differential ASV abundance was assessed using negative binomial Wald tests and P values were adjusted using the Benjamini and Hochberg false-discovery rate correction with a significance cut-off of P &lt; 0.01. ASVs shown with a log2-fold change greater than zero are significantly more abundant in individuals without this allele and ASVs with a log2 fold change smaller than zero are significantly more abundant in individuals with a copy of this allele.
DOI: 10.6084/m9.figshare.19321400
title: Additional file 1 of Spatiotemporal analysis of dengue fever in Burkina Faso from 2016 to 2019

description: Additional file 1. Dengue annual cases by health district in Burkina Faso. This database contains by year for each health district in Burkina Faso, the dengue cases, the population, the average and smoothed incidences and excess hazard risk of dengue.
DOI: 10.6084/m9.figshare.19321400.v1
title: Additional file 1 of Spatiotemporal analysis of dengue fever in Burkina Faso from 2016 to 2019

description: Additional file 1. Dengue annual cases by health district in Burkina Faso. This database contains by year for each health district in Burkina Faso, the dengue cases, the population, the average and smoothed incidences and excess hazard risk of dengue.
DOI: 10.6084/m9.figshare.19196330
title: Whole-cell segmentations for Cytotoxic T lymphocyte attacking a cancer cell (jrc_ctl-id8-3)

description: Cytotoxic T lymphocytes (CTLs) kill virus-infected and tumorigenic cells through the polarized release of perforin and granzymes, which are housed in modified lysosomes called lytic granules. Perforin is a pore-forming toxin that creates an ephemeral portal in the plasma membrane of the target through which granzymes enter the cytosol and initiate apoptosis. This conjugate was captured moments after perforin secretion toward the target. Sample: OT-I mouse cytotoxic T lymphocyte attacking an ID8 ovarian cancer cell; fixed and imaged moments after the release of perforin/granzyme from lytic granules. The ID8 murine ovarian cancer cell is stably expressing mEmerald-Chmp4b and TOMM20-SNAP. Protocol: High pressure freezing, freeze-substitution resin embedding with 2% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Alex Ritter (Genentech), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia). Segmentations by Ariadne.ai.Dataset ID: jrc_ctl-id8-3Final voxel size (nm): 8 x 8 x 8 (X, Y, Z)Dimensions (µm): 70 x 12.8 x 32.24 (X, Y, Z)Acquisition date: 2020-02-12Dataset URL: Visualization Website: https://openorganelle.janelia.org/datasets/jrc_ctl-id8-3<br>Publication: Ritter et al., ESCRT-mediated membrane repair at the immunological synapse protects tumor cells against T cell attack, Science (2022).<br>