cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13296979
title: Additional file 2 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 2. List of all expressed genes in the RNA-seq and proteomics datasets. Excel file (.xls) with all genes and proteins that were deemed expressed, as defined in Methods, and used in the downstream analysis and visualization of data. The worksheet named “RNA_seq_whole expressed” contains the data from the RNA-seq experiments (expression values in RPKM), and differential expression analysis results. The worksheet named “Proteomics_whole expressed” contains the data from the label-free proteomic experiments (expression values in iBAQ), and differential expression analysis results.
DOI: 10.6084/m9.figshare.13296979.v1
title: Additional file 2 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 2. List of all expressed genes in the RNA-seq and proteomics datasets. Excel file (.xls) with all genes and proteins that were deemed expressed, as defined in Methods, and used in the downstream analysis and visualization of data. The worksheet named “RNA_seq_whole expressed” contains the data from the RNA-seq experiments (expression values in RPKM), and differential expression analysis results. The worksheet named “Proteomics_whole expressed” contains the data from the label-free proteomic experiments (expression values in iBAQ), and differential expression analysis results.
DOI: 10.6084/m9.figshare.13296976
title: Additional file 1 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 1. Gene set enrichment analysis. The Excel file (.xls) shows the output of gene set enrichment analysis (GSEA) [49, 50] of pre-ranked gene lists from the rat LSEC and KC RNA-seq datasets, associated with Gene Ontology (GO) biological processes (BP). The genes were pre-ranked based on expression. We have used the C5 collection of annotated gene sets in the Molecular Signatures Database (release 6.2; BP) [53] which consists of gene sets derived from GO [51, 52]. Name of worksheets: “GSEA_plot”, “GSEA_RNAseq_LSEC_BP”, and “GSEA_RNAseq_KC_BP”. The worksheet named “GSEA_Plot” contains the selected enriched BPs shown in Fig. 4.
DOI: 10.6084/m9.figshare.13296976.v1
title: Additional file 1 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 1. Gene set enrichment analysis. The Excel file (.xls) shows the output of gene set enrichment analysis (GSEA) [49, 50] of pre-ranked gene lists from the rat LSEC and KC RNA-seq datasets, associated with Gene Ontology (GO) biological processes (BP). The genes were pre-ranked based on expression. We have used the C5 collection of annotated gene sets in the Molecular Signatures Database (release 6.2; BP) [53] which consists of gene sets derived from GO [51, 52]. Name of worksheets: “GSEA_plot”, “GSEA_RNAseq_LSEC_BP”, and “GSEA_RNAseq_KC_BP”. The worksheet named “GSEA_Plot” contains the selected enriched BPs shown in Fig. 4.
DOI: 10.6084/m9.figshare.13296991.v1
title: Additional file 6 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 6. Immune regulatory factors. Excel file (.xls) with the list of expressed genes annotated to cytokine receptor binding (GO:0005126), cytokine receptor activity (GO:0004896), complement activation (GO:0006956), or complement receptor activity (GO:0004875) in rat LSECs and KCs. The file shows their corresponding abundance in the RNA-seq datasets (RPKM values; worksheet named “Immunereg.factors_RPKM_RNAseq”) and label-free proteomics datasets (iBAQ values; worksheet named “Immunereg.factors_iBAQ_LFP”) along with differential expression analysis outputs. For visualization of the selected genes shown in Fig. 7, log2(RPKM+ 1) was used.
DOI: 10.6084/m9.figshare.13296991
title: Additional file 6 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 6. Immune regulatory factors. Excel file (.xls) with the list of expressed genes annotated to cytokine receptor binding (GO:0005126), cytokine receptor activity (GO:0004896), complement activation (GO:0006956), or complement receptor activity (GO:0004875) in rat LSECs and KCs. The file shows their corresponding abundance in the RNA-seq datasets (RPKM values; worksheet named “Immunereg.factors_RPKM_RNAseq”) and label-free proteomics datasets (iBAQ values; worksheet named “Immunereg.factors_iBAQ_LFP”) along with differential expression analysis outputs. For visualization of the selected genes shown in Fig. 7, log2(RPKM+ 1) was used.
DOI: 10.6084/m9.figshare.13296982.v1
title: Additional file 3 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 3. Genes and proteins associated with immune system processes. Excel file (.xls) with the list of genes and proteins associated with the term immune system processes (GO:0002376) presented in the two heatmaps in Fig. 5a, along with their associated expression values (RPKM, or iBAQ). The two worksheets are named “Immune genes_RPKM_RNAseq”, and “Immune genes_iBAQ_proteomics”. Of note, for visualization, log2(RPKM+ 1) and log2(iBAQ+ 1) were used in the heatmaps in Fig. 5a.
DOI: 10.6084/m9.figshare.13297000
title: Additional file 9 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 9. Analysis of microarray expression data obtained from Nolan et al. 2013 [35]. Excel file (.xls) with the comparative analysis of expression data obtained from a microarray profiling study of mouse (Mus musculus) primary microvascular endothelial cells, published by Nolan DJ, Ginsberg M, Israely E, Palikuqi B, Poulos MG, James D, et al. Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration [35]. The microarray data was downloaded from the GEO public database-Series GSE47067. Title of dataset: In vivo endothelial cell heterogeneity. The first worksheet, named “Pairwise_DGE (Nolan_2013)”, shows pairwise analysis of the expression data of endothelial cells from different organs. The second worksheet, named “DAVID_ liver specific genes”, presents the DAVID enrichment analysis [54, 55] output of genes that were consistently significantly abundant in mouse liver sinusoidal endothelial cells (LSECs) in every pairwise comparison of LSECs with other microvascular endothelial cells in the dataset (Significance level: FDR ≤ 0.05, and log2 fold change ≥1).
DOI: 10.6084/m9.figshare.13296985.v1
title: Additional file 4 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 4. Scavenger receptors and C-type lectins. Excel file (.xls) with the list of genes and proteins presented in the two heatmaps in Fig. 6a, along with their associated expression values (RPKM, or iBAQ). The two worksheets are named “SRs&lections_RPKM_RNAseq) and “SRs&lectins_iBAQ_proteomics”. For visualization, log2(RPKM+ 1) and log2(iBAQ+ 1) were used in Fig. 6.
DOI: 10.6084/m9.figshare.13297000.v1
title: Additional file 9 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 9. Analysis of microarray expression data obtained from Nolan et al. 2013 [35]. Excel file (.xls) with the comparative analysis of expression data obtained from a microarray profiling study of mouse (Mus musculus) primary microvascular endothelial cells, published by Nolan DJ, Ginsberg M, Israely E, Palikuqi B, Poulos MG, James D, et al. Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration [35]. The microarray data was downloaded from the GEO public database-Series GSE47067. Title of dataset: In vivo endothelial cell heterogeneity. The first worksheet, named “Pairwise_DGE (Nolan_2013)”, shows pairwise analysis of the expression data of endothelial cells from different organs. The second worksheet, named “DAVID_ liver specific genes”, presents the DAVID enrichment analysis [54, 55] output of genes that were consistently significantly abundant in mouse liver sinusoidal endothelial cells (LSECs) in every pairwise comparison of LSECs with other microvascular endothelial cells in the dataset (Significance level: FDR ≤ 0.05, and log2 fold change ≥1).
DOI: 10.6084/m9.figshare.13296994.v1
title: Additional file 7 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 7. Genes annotated to antigen processing and presentation and lymphocyte co-stimulation. Excel file (.xls) with the list of expressed genes associated with antigen processing and presentation (GO:0019882), and lymphocyte co-stimulation (GO:0031294) in LSECs and KCs. The file shows their corresponding abundance in the RNA-seq datasets (RPKM values; worksheet named “Immuneactivation_RPKM_RNAseq”) and label-free proteomics datasets (iBAQ values; worksheet named “Immuneactivation_iBAQ_LFP”) along with differential expression analysis outputs. For visualization of the selected genes and proteins shown in Fig. 8, log2 (RPKM+ 1), and log2 (iBAQ+ 1) were used.
DOI: 10.6084/m9.figshare.13296994
title: Additional file 7 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

description: Additional file 7. Genes annotated to antigen processing and presentation and lymphocyte co-stimulation. Excel file (.xls) with the list of expressed genes associated with antigen processing and presentation (GO:0019882), and lymphocyte co-stimulation (GO:0031294) in LSECs and KCs. The file shows their corresponding abundance in the RNA-seq datasets (RPKM values; worksheet named “Immuneactivation_RPKM_RNAseq”) and label-free proteomics datasets (iBAQ values; worksheet named “Immuneactivation_iBAQ_LFP”) along with differential expression analysis outputs. For visualization of the selected genes and proteins shown in Fig. 8, log2 (RPKM+ 1), and log2 (iBAQ+ 1) were used.
DOI: 10.6084/m9.figshare.13297039
title: Additional file 2 of Phase II randomized trial of capecitabine with bevacizumab and external beam radiation therapy as preoperative treatment for patients with resectable locally advanced rectal adenocarcinoma: long term results

description: Additional file 2: Supplementary Figure 2. DFS. N-downstaging and treatment arm.
DOI: 10.6084/m9.figshare.13297039.v1
title: Additional file 2 of Phase II randomized trial of capecitabine with bevacizumab and external beam radiation therapy as preoperative treatment for patients with resectable locally advanced rectal adenocarcinoma: long term results

description: Additional file 2: Supplementary Figure 2. DFS. N-downstaging and treatment arm.
DOI: 10.6084/m9.figshare.13297036
title: Additional file 1 of Phase II randomized trial of capecitabine with bevacizumab and external beam radiation therapy as preoperative treatment for patients with resectable locally advanced rectal adenocarcinoma: long term results

description: Additional file 1: Supplementary Figure 1. DFS – T-downstaging and treatment arm
DOI: 10.6084/m9.figshare.13297036.v1
title: Additional file 1 of Phase II randomized trial of capecitabine with bevacizumab and external beam radiation therapy as preoperative treatment for patients with resectable locally advanced rectal adenocarcinoma: long term results

description: Additional file 1: Supplementary Figure 1. DFS – T-downstaging and treatment arm
DOI: 10.6084/m9.figshare.13297048.v1
title: Additional file 3 of Potentially inappropriate testing for vitamin D deficiency: a cross-sectional study in Switzerland

description: Additional file 3: Table S3. Percentage of population that received testing for vitamin D in 2015 and 2018, stratified by age group, and ratio between 2015 and 2018.
DOI: 10.6084/m9.figshare.13297048
title: Additional file 3 of Potentially inappropriate testing for vitamin D deficiency: a cross-sectional study in Switzerland

description: Additional file 3: Table S3. Percentage of population that received testing for vitamin D in 2015 and 2018, stratified by age group, and ratio between 2015 and 2018.
DOI: 10.6084/m9.figshare.13297098.v1
title: Additional file 2 of Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

description: Additional file 2: Supplementary Table S1. Results of taxonomic classification of sequences conducted with Kraken2.
DOI: 10.6084/m9.figshare.13297101
title: Additional file 3 of Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

description: Additional file 3: Supplementary Table S2. Annotation of MetaBat2 bins and relative abundance in each sample.
DOI: 10.6084/m9.figshare.13297098
title: Additional file 2 of Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

description: Additional file 2: Supplementary Table S1. Results of taxonomic classification of sequences conducted with Kraken2.
DOI: 10.6084/m9.figshare.13297104
title: Additional file 4 of Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

description: Additional file 4: Supplementary Table S3. Annotation and relative abundance of predicted proteins upon alignments against several protein databases.
DOI: 10.6084/m9.figshare.13297101.v1
title: Additional file 3 of Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

description: Additional file 3: Supplementary Table S2. Annotation of MetaBat2 bins and relative abundance in each sample.
DOI: 10.6084/m9.figshare.13297104.v1
title: Additional file 4 of Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

description: Additional file 4: Supplementary Table S3. Annotation and relative abundance of predicted proteins upon alignments against several protein databases.
DOI: 10.6084/m9.figshare.13297158
title: Additional file 1 of Health behaviors in major chronic diseases patients: trends and regional variations analysis, 2008–2017, Korea

description: Additional file 1.
DOI: 10.6084/m9.figshare.13297158.v1
title: Additional file 1 of Health behaviors in major chronic diseases patients: trends and regional variations analysis, 2008–2017, Korea

description: Additional file 1.
DOI: 10.6084/m9.figshare.13297200
title: Additional file 1 of An aggressive systemic mastocytosis preceded by ovarian dysgerminoma

description: Additional file 1: Table S1. PCR primers used in this study. Table S2. BM-1-specific candidate variants of cancer-related genes analyzed by Mutect2. Table S3. Candidate variants of cancer-related genes identified in the PB of the study patient.
DOI: 10.6084/m9.figshare.13297200.v1
title: Additional file 1 of An aggressive systemic mastocytosis preceded by ovarian dysgerminoma

description: Additional file 1: Table S1. PCR primers used in this study. Table S2. BM-1-specific candidate variants of cancer-related genes analyzed by Mutect2. Table S3. Candidate variants of cancer-related genes identified in the PB of the study patient.
DOI: 10.6084/m9.figshare.13297300
title: Additional file 1 of Building a rapid autopsy program – a step-by-step logistics guide

description: Additional file 1: Supplementary Table S1.
DOI: 10.6084/m9.figshare.13297300.v1
title: Additional file 1 of Building a rapid autopsy program – a step-by-step logistics guide

description: Additional file 1: Supplementary Table S1.
DOI: 10.6084/m9.figshare.13297321
title: Additional file 2 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 2: Table S1: Raw data and LSMeans for scald susceptibility.
DOI: 10.6084/m9.figshare.13297327.v1
title: Additional file 4 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 4: Table S3: GWAS results including all markers that were detected in at least one cross-validation run.
DOI: 10.6084/m9.figshare.13297330.v1
title: Additional file 5 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 5: Table S4: Family-specific effects of eight major scald QTL defined in GWAS.
DOI: 10.6084/m9.figshare.13297324.v1
title: Additional file 3 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 3: Table S2: Genotyping results of HEB-25 parents with locus-specific markers.
DOI: 10.6084/m9.figshare.13297333.v1
title: Additional file 6 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 6: Table S5: Summary of reported scald resistance genes and QTLs.
DOI: 10.6084/m9.figshare.13297339
title: Additional file 8 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 8: Table S6: Barleymap output of high confidence candidate genes for each of the eight major QTLs.
DOI: 10.6084/m9.figshare.13297339.v1
title: Additional file 8 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 8: Table S6: Barleymap output of high confidence candidate genes for each of the eight major QTLs.
DOI: 10.6084/m9.figshare.13297333
title: Additional file 6 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 6: Table S5: Summary of reported scald resistance genes and QTLs.
DOI: 10.6084/m9.figshare.13297321.v1
title: Additional file 2 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 2: Table S1: Raw data and LSMeans for scald susceptibility.
DOI: 10.6084/m9.figshare.13297330
title: Additional file 5 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 5: Table S4: Family-specific effects of eight major scald QTL defined in GWAS.
DOI: 10.6084/m9.figshare.13297327
title: Additional file 4 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 4: Table S3: GWAS results including all markers that were detected in at least one cross-validation run.
DOI: 10.6084/m9.figshare.13297324
title: Additional file 3 of Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

description: Additional file 3: Table S2: Genotyping results of HEB-25 parents with locus-specific markers.
DOI: 10.6084/m9.figshare.13297369
title: Additional file 4 of Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration

description: Additional file 4: Table S2. Annotation of differentially expressed unigenes (DEUs) between NSS and others.
DOI: 10.6084/m9.figshare.13297353
title: Additional file 1 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 1: Table S1. Strains used in this study and their characteristics.
DOI: 10.6084/m9.figshare.13297353.v1
title: Additional file 1 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 1: Table S1. Strains used in this study and their characteristics.
DOI: 10.6084/m9.figshare.13297368
title: Additional file 6 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 6: Table S5. Associations with resistance phenotypes based on treeWAS results for accessory genes, SNPs in core genes and whole-genome SNPs; or based on Kleborate or direct analysis of potential target sequences.
DOI: 10.6084/m9.figshare.13297368.v1
title: Additional file 6 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 6: Table S5. Associations with resistance phenotypes based on treeWAS results for accessory genes, SNPs in core genes and whole-genome SNPs; or based on Kleborate or direct analysis of potential target sequences.
DOI: 10.6084/m9.figshare.13297356.v1
title: Additional file 2 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 2: Table S2. Antimicrobial agents and zone diameters interpretative breakpoints used.
DOI: 10.6084/m9.figshare.13297359
title: Additional file 3 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 3: Table S3. Susceptibility data and interpretative categories based on current EUCAST recommendations (SIR) and proposed ecological cutoffs (ECOFF).
DOI: 10.6084/m9.figshare.13297365
title: Additional file 5 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 5: Table S4. Molecular explanations for non-toxigenic tox gene-bearing (NTTB) strains.
DOI: 10.6084/m9.figshare.13297371
title: Additional file 7 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 7: Table S6. Susceptibility phenotypes of transformed C. glutamicum ATCC 13032 strains.
DOI: 10.6084/m9.figshare.13297374
title: Additional file 8 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 8: Table S7. Detection of the pbp2m gene in other Corynebacterium genomes.
DOI: 10.6084/m9.figshare.13297371.v1
title: Additional file 7 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 7: Table S6. Susceptibility phenotypes of transformed C. glutamicum ATCC 13032 strains.
DOI: 10.6084/m9.figshare.13297374.v1
title: Additional file 8 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 8: Table S7. Detection of the pbp2m gene in other Corynebacterium genomes.
DOI: 10.6084/m9.figshare.13297359.v1
title: Additional file 3 of Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

description: Additional file 3: Table S3. Susceptibility data and interpretative categories based on current EUCAST recommendations (SIR) and proposed ecological cutoffs (ECOFF).