cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3659036_d2
title: Additional file 4: of LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

description: Lists of DEGs between LPS stimulated and unstimulated PBMCs. For every effect studied (LPS, and interaction effects: LPS:Fam1, LPS:Fam2) the list of genes differentially expressed at false discovery rate
DOI: 10.6084/m9.figshare.c.3659033_d2
title: Additional file 2: of Evolutionary diversification of Pseudomonas aeruginosa in an artificial sputum model

description: Antimicrbial susceptibility data and data for beta-lactamase production. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3659036_d6.v1
title: Additional file 6: of LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

description: Co-expressed gene modules. For every module the list of genes with module membership, and FDR values of the module association with LPS stimulation and cohort is given. (XLSX 6286Â kb)
DOI: 10.6084/m9.figshare.c.3659036_d6
title: Additional file 6: of LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

description: Co-expressed gene modules. For every module the list of genes with module membership, and FDR values of the module association with LPS stimulation and cohort is given. (XLSX 6286Â kb)
DOI: 10.6084/m9.figshare.c.3659081_d1.v1
title: Additional file 2: Table S1-S3. of A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients

description: Table S1. A summary of significant primary biliary cholangitis (PBC) loci selected based on GWAS results replicated by individual patient TaqMan genotyping. Position - position of a given loci on chromosome (GRCh37); GENESYMBOL - symbol of a gene SNP is located in, provided SNP is located within gene; PRECEDESYMBOL/FOLLOWSYMBOL - symbol of genes flanking given SNP, p-value - result of TagMan replication assessed with Fisher’s exact test; OR - odds ratio; PBC vs control (1st/2nd analysis) - indication whether given SNP met selection criterion in GWAS analysis, 1 = YES. Yellow marks SNPs significant in ‘PSC vs control’ comparison. Table S2. A summary of primary sclerosing cholangitis (PSC) loci selected based on GWAS results replicated by individual patient TaqMan genotyping. Position - position of a given loci on chromosome (GRCh37); GENESYMBOL - symbol of a gene SNP is located in, provided SNP is located within gene; PRECEDESYMBOL/FOLLOWSYMBOL - symbol of genes flanking given SNP, p-value - result of TaqMan replication assessed with Fisher’s exact test; OR - odds ratio; PSC vs control (1st/2nd analysis) - indication whether given SNP met selection criterion in GWAS analysis, 1 = YES. Yellow marks SNPs significant in ‘PBC vs control’ comparison. Table S3. Swiss-Prot Protein Information Resource Terms significantly overrepresented among genes associated with PBC and PSC in this study. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3659081_d1
title: Additional file 2: Table S1-S3. of A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients

description: Table S1. A summary of significant primary biliary cholangitis (PBC) loci selected based on GWAS results replicated by individual patient TaqMan genotyping. Position - position of a given loci on chromosome (GRCh37); GENESYMBOL - symbol of a gene SNP is located in, provided SNP is located within gene; PRECEDESYMBOL/FOLLOWSYMBOL - symbol of genes flanking given SNP, p-value - result of TagMan replication assessed with Fisher’s exact test; OR - odds ratio; PBC vs control (1st/2nd analysis) - indication whether given SNP met selection criterion in GWAS analysis, 1 = YES. Yellow marks SNPs significant in ‘PSC vs control’ comparison. Table S2. A summary of primary sclerosing cholangitis (PSC) loci selected based on GWAS results replicated by individual patient TaqMan genotyping. Position - position of a given loci on chromosome (GRCh37); GENESYMBOL - symbol of a gene SNP is located in, provided SNP is located within gene; PRECEDESYMBOL/FOLLOWSYMBOL - symbol of genes flanking given SNP, p-value - result of TaqMan replication assessed with Fisher’s exact test; OR - odds ratio; PSC vs control (1st/2nd analysis) - indication whether given SNP met selection criterion in GWAS analysis, 1 = YES. Yellow marks SNPs significant in ‘PBC vs control’ comparison. Table S3. Swiss-Prot Protein Information Resource Terms significantly overrepresented among genes associated with PBC and PSC in this study. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3659078_d2.v1
title: Additional file 1: Table S1. of Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment

description: List of the core genes chosen for the whole genome phylogenetic analysis. This list is composed of 499 orthologous genes from 20 genomes within the phylum Thermotogae. (XLS 210Â kb)
DOI: 10.15468/dl.zqsvrs
title: Occurrence Download

description: A dataset containing 3372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Parambassis siamensis (Fowler, 1937), Pristolepis fasciata (Bleeker, 1851), Esomus metallicus Ahl, 1923)",
 "Year is not null",
 {
 "not" : {
 "Issue" : [
 "is one of (Recorded date invalid, Taxon match fuzzy, Taxon match higher rank)"
 ]
 }
 }
 ]
}

 The dataset includes 3372 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038037-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3659087_d3
title: Additional file 5: Table S4. of Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types

description: Table S4. Annotation of the 39 unreported genes. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3659087_d5.v1
title: Additional file 4: Table S3. of Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types

description: Overlay of previous cell cycle gene lists on the clusters. (XLSX 75Â kb)
DOI: 10.6084/m9.figshare.c.3659087_d5
title: Additional file 4: Table S3. of Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types

description: Overlay of previous cell cycle gene lists on the clusters. (XLSX 75Â kb)
DOI: 10.6084/m9.figshare.c.3659126_d1.v1
title: Additional file 1: of Approval status and evidence for WHO essential medicines for children in the United States, United Kingdom, and Japan: a cross-sectional study

description: Approval status in the United States, United Kingdom, and Japan and supporting evidence for medicines on the 5th WHO Model List of Essential Medicines for Children. (XLSX 33Â kb)
DOI: 10.6084/m9.figshare.c.3659126_d1
title: Additional file 1: of Approval status and evidence for WHO essential medicines for children in the United States, United Kingdom, and Japan: a cross-sectional study

description: Approval status in the United States, United Kingdom, and Japan and supporting evidence for medicines on the 5th WHO Model List of Essential Medicines for Children. (XLSX 33Â kb)
DOI: 10.6084/m9.figshare.c.3659156_d1.v1
title: Additional file 7: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Differentially expressed genes between flubendiamide-treated and control ACBs. (XLS 27928Â kb)
DOI: 10.6084/m9.figshare.c.3659141_d4
title: Additional file 4: Table S2. of Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

description: Northern blot validation of sRNAs. The table summarizes the sRNAs that were confirmed via Northern blot analysis. The sRNAs location, category, sizes and associated genes are indicated. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3659141_d4.v1
title: Additional file 4: Table S2. of Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

description: Northern blot validation of sRNAs. The table summarizes the sRNAs that were confirmed via Northern blot analysis. The sRNAs location, category, sizes and associated genes are indicated. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3659156_d1
title: Additional file 7: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Differentially expressed genes between flubendiamide-treated and control ACBs. (XLS 27928Â kb)
DOI: 10.6084/m9.figshare.c.3659141_d5.v1
title: Additional file 10: Table S3. of Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

description: Genes with antisense and 5′ UTR sRNAs. The table contains information about all of the genes with antisense and 5′ UTR sRNAs associated with them. Gene ontology terms (GO terms) for biological processes (BP) are also given for each gene. The column titled, “Norgard FoldChange” contains the fold-change of that particular gene as reported by Revel et al. [52] via microarray after a temperature shift. (XLSX 221 kb)
DOI: 10.6084/m9.figshare.c.3659141_d5
title: Additional file 10: Table S3. of Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

description: Genes with antisense and 5′ UTR sRNAs. The table contains information about all of the genes with antisense and 5′ UTR sRNAs associated with them. Gene ontology terms (GO terms) for biological processes (BP) are also given for each gene. The column titled, “Norgard FoldChange” contains the fold-change of that particular gene as reported by Revel et al. [52] via microarray after a temperature shift. (XLSX 221 kb)
DOI: 10.15468/dl.8r6ag2
title: Occurrence Download

description: A dataset containing 3372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Parambassis siamensis (Fowler, 1937), Pristolepis fasciata (Bleeker, 1851), Esomus metallicus Ahl, 1923)",
 "Year is not null",
 {
 "not" : {
 "Issue" : [
 "is one of (Recorded date invalid, Taxon match fuzzy, Taxon match higher rank)"
 ]
 }
 }
 ]
}

 The dataset includes 3372 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038038-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3659156_d2
title: Additional file 6: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Nucleotide sequences of the target sites of the most important insecticide classes. (TXT 25Â kb)
DOI: 10.6084/m9.figshare.c.3659156_d2.v1
title: Additional file 6: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Nucleotide sequences of the target sites of the most important insecticide classes. (TXT 25Â kb)
DOI: 10.6084/m9.figshare.c.3659156_d3.v1
title: Additional file 5: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Carboxyl/cholinesterase nucleotide sequences of the ACB. (TXT 43Â kb)
DOI: 10.6084/m9.figshare.c.3659156_d3
title: Additional file 5: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Carboxyl/cholinesterase nucleotide sequences of the ACB. (TXT 43Â kb)
DOI: 10.15468/dl.8xppxw
title: Occurrence Download

description: A dataset containing 3372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Parambassis siamensis (Fowler, 1937), Pristolepis fasciata (Bleeker, 1851), Esomus metallicus Ahl, 1923)",
 "Year is not null",
 {
 "not" : {
 "Issue" : [
 "is one of (Recorded date invalid, Taxon match fuzzy, Taxon match higher rank)"
 ]
 }
 }
 ]
}

 The dataset includes 3372 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038039-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3659156_d7.v1
title: Additional file 4: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Glutathione S-transferase nucleotide sequences of the ACB. (TXT 17Â kb)
DOI: 10.6084/m9.figshare.c.3659156_d7
title: Additional file 4: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Glutathione S-transferase nucleotide sequences of the ACB. (TXT 17Â kb)
DOI: 10.15468/dl.bmdugv
title: Occurrence Download

description: A dataset containing 9725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Occurrence evidence, Human Observation, Machine Observation)",
 "StateProvince is one of (Nevada, Nevada (State), Nevada (NV))",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 9725 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038040-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3659156_d8.v1
title: Additional file 3: of 
                     De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes

description: Cytochrome P450 nucleotide sequences of the ACB. (TXT 48Â kb)
DOI: 10.6084/m9.figshare.28049693
title: Agave weberi raw GC-MS files

description: Metabolite extraction from Agave weberi leaf tissue
DOI: 10.6084/m9.figshare.28049693.v1
title: Agave weberi raw GC-MS files

description: Metabolite extraction from Agave weberi leaf tissue
DOI: 10.6084/m9.figshare.c.3659189_d5.v1
title: Additional file 4: of Genetic architecture of kernel composition in global sorghum germplasm

description: Protein, fat, and starch content of sorghum accessions. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3659219_d1.v1
title: Additional file 1: of Prospective cohort study of procalcitonin levels in children with cancer presenting with febrile neutropenia

description: Procalcitonin study data. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.c.3659189_d5
title: Additional file 4: of Genetic architecture of kernel composition in global sorghum germplasm

description: Protein, fat, and starch content of sorghum accessions. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3659228_d3.v1
title: Additional file 6: of Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

description: Primers used in this study. (XLS 38Â kb)
DOI: 10.6084/m9.figshare.c.3659231_d3
title: Additional file 2: of Unsupervised statistical discovery of spaced motifs in prokaryotic genomes

description: Table S2.. Significant motif pairs detected in 569 analyzed genomes. Description of data: The table contains 3326 motif pairs in 569 genomes that identified as significant by our approach. (CSV 300 kb)
DOI: 10.6084/m9.figshare.c.3659228_d3
title: Additional file 6: of Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

description: Primers used in this study. (XLS 38Â kb)
DOI: 10.6084/m9.figshare.c.3659237_d1.v1
title: Additional file 1: of Availability of essential medicines in selected public, primary and secondary health care institutions of a rural Sri Lankan district: a spot survey

description: Availability of essential medicines in a rural Sri Lankan district, 2016. This provides the results of the entire survey with data for each essential medicine. (XLS 187Â kb)
DOI: 10.6084/m9.figshare.c.3659237_d1
title: Additional file 1: of Availability of essential medicines in selected public, primary and secondary health care institutions of a rural Sri Lankan district: a spot survey

description: Availability of essential medicines in a rural Sri Lankan district, 2016. This provides the results of the entire survey with data for each essential medicine. (XLS 187Â kb)
DOI: 10.6084/m9.figshare.c.3659243_d1.v1
title: Additional file 19: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: SNP alignment from the REALPHY phyML analysis with NC000913 and NC012759 as reference genomes. (FASTA 85 kb)
DOI: 10.6084/m9.figshare.c.3659243_d1
title: Additional file 19: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: SNP alignment from the REALPHY phyML analysis with NC000913 and NC012759 as reference genomes. (FASTA 85 kb)
DOI: 10.6084/m9.figshare.c.3659228_d6.v1
title: Additional file 8: of Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

description: Normalized data all entities 8x60k. (TXT 11290Â kb)
DOI: 10.6084/m9.figshare.c.3659261_d1.v1
title: Additional file 1: of Is non-HDL-cholesterol a better predictor of long-term outcome in patients after acute myocardial infarction compared to LDL-cholesterol? : a retrospective study

description: Non HDL-C vs LDL-C and long term outcomes. The dataset for the non-HDL-C and LDL-C on long term cardiovascular outcomes after AMI analysis. (XLS 338 kb)
DOI: 10.6084/m9.figshare.c.3659243_d6.v1
title: Additional file 23: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: Tab separated table showing all results from the new tree comparison method, where matching parent/child relations and matching clades to the benchmark child list are counted. The cutoff branch length is optimized. (TXT 6 kb)
DOI: 10.6084/m9.figshare.c.3659261_d1
title: Additional file 1: of Is non-HDL-cholesterol a better predictor of long-term outcome in patients after acute myocardial infarction compared to LDL-cholesterol? : a retrospective study

description: Non HDL-C vs LDL-C and long term outcomes. The dataset for the non-HDL-C and LDL-C on long term cardiovascular outcomes after AMI analysis. (XLS 338 kb)
DOI: 10.6084/m9.figshare.c.3659243_d6
title: Additional file 23: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: Tab separated table showing all results from the new tree comparison method, where matching parent/child relations and matching clades to the benchmark child list are counted. The cutoff branch length is optimized. (TXT 6 kb)
DOI: 10.6084/m9.figshare.c.3659243_d7.v1
title: Additional file 7: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: a Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_017641 used as reference. PDF. b Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_017641 used as reference. Newick file. (ZIP 5 kb)
DOI: 10.6084/m9.figshare.c.3659243_d7
title: Additional file 7: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: a Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_017641 used as reference. PDF. b Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_017641 used as reference. Newick file. (ZIP 5 kb)
DOI: 10.6084/m9.figshare.c.3659243_d11.v1
title: Additional file 6: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: a Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_012759 used as reference. PDF. b Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_012759 used as reference. Newick file. (ZIP 5 kb)
DOI: 10.6084/m9.figshare.c.3659243_d11
title: Additional file 6: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: a Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_012759 used as reference. PDF. b Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, E. coli NC_012759 used as reference. Newick file. (ZIP 5 kb)
DOI: 10.6084/m9.figshare.c.3659243_d12.v1
title: Additional file 20: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: Position for mutations from S19 SNP alignment. Positions related to NC000913. (TXT 5 kb)
DOI: 10.6084/m9.figshare.c.3659243_d12
title: Additional file 20: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: Position for mutations from S19 SNP alignment. Positions related to NC000913. (TXT 5 kb)
DOI: 10.6084/m9.figshare.c.3659243_d14.v1
title: Additional file 18: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: SNP alignment from the CSI Phylogeny analysis with NC000913 as reference genome. (FASTA 44 kb)
DOI: 10.6084/m9.figshare.c.3659243_d13.v1
title: Additional file 22: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: The benchmark child list with the known tree structure for the experiment, which all of the trees inferred on all the 101 strains was compared to. Tab separated. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3659243_d13
title: Additional file 22: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: The benchmark child list with the known tree structure for the experiment, which all of the trees inferred on all the 101 strains was compared to. Tab separated. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3659243_d14
title: Additional file 18: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: SNP alignment from the CSI Phylogeny analysis with NC000913 as reference genome. (FASTA 44 kb)
DOI: 10.6084/m9.figshare.c.3659243_d21
title: Additional file 14: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: SNP alignment from the NDtree analysis with contigs from day 1 as reference genome. (FASTA 40 kb)
DOI: 10.6084/m9.figshare.c.3659243_d22
title: Additional file 24: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: The full results from the cutoff optimization. (TXT 6 kb)
DOI: 10.6084/m9.figshare.c.3659243_d23.v1
title: Additional file 3: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: a Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, contigs from day 1 used as reference. PDF. b Tree inferred by NDtree, Z-score 1.96, Neighbor Joining tree, contigs from day 1 used as reference. Newick file. (ZIP 5 kb)
DOI: 10.6084/m9.figshare.c.3659243_d24.v1
title: Additional file 25: of Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

description: Tab separated table, showing results from the new tree comparison method when the cutoff was set to 0. (TXT 2 kb)