cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6132452
title: Additional file 28: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S3. Correlation between differentially abundant bacteria in CRC. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.6132452.v1
title: Additional file 28: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S3. Correlation between differentially abundant bacteria in CRC. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.6132461
title: Additional file 29: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S8. Significant correlations between CRC-enriched bacteria and KO categories. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.6132461.v1
title: Additional file 29: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S8. Significant correlations between CRC-enriched bacteria and KO categories. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.6132479
title: Additional file 3: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S14. Significance of the abundance changes with rank sum test. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6132479.v1
title: Additional file 3: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S14. Significance of the abundance changes with rank sum test. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6132488
title: Additional file 4: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S4. Correlation between differentially abundant bacteria in early CRC. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.6132488.v1
title: Additional file 4: of Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers

description: Table S4. Correlation between differentially abundant bacteria in early CRC. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.6133121
title: Weighted normalized UniFrac distances

description: The weighted normalized UniFrac distance (Lozupone et al AEM 2007) matrix of the 9511 fecal samples used in the American Gut paper. UniFrac was computed using Striped UniFrac (https://github.com/biocore/unifrac). Prior to execution of UniFrac, Deblur (Amir et al mSystems 2017) was run on the samples, all bloom sOTUs were removed (Amir et al mSystems 2017), and samples were rarefied to a depth of 1250 reads (Weiss et al Microbiome 2017). For the phylogeny, fragments were inserted using SEPP (Mirarab et al Pac Symp Biocomput 2012) into the Greengenes 13_5 99% OTU tree (McDonald et al ISME 2012).
DOI: 10.6084/m9.figshare.6137192
title: American Gut Project fecal sOTU counts table

description: The Deblur sOTU counts table for the fecal samples used in the American Gut Project manuscript. The samples were trimmed to a common read length of 125nt, and processed by Deblur (Amir et al mSystems 2017). Blooms were removed (Amir et al mSystems 2017) and any sample with fewer than 1250 sequences was omitted. This table is not rarefied,.
DOI: 10.6084/m9.figshare.6137198
title: American Gut Project fecal sOTU relative abundance table

description: The Deblur sOTU relative abundance table for the fecal samples used in the American Gut Project manuscript. The samples were trimmed to a common read length of 125nt, and processed by Deblur (Amir et al mSystems 2017). Blooms were removed (Amir et al mSystems 2017) and any sample with fewer than 1250 sequences was omitted. This table is not rarefied, and is normalized to 1.
DOI: 10.6084/m9.figshare.6137270
title: ag_tree.tre

description: The SEPP (Mirarab et al Pac Symp Biocomput 2012) fragment insertion tree used for phylogenetic analyses.
DOI: 10.6084/m9.figshare.6137312
title: American Gut collated alpha diversities

description: Collated alpha diversity values for the 9511 fecal samples used in the American Gut Project manuscript.
DOI: 10.6084/m9.figshare.6137315
title: Full American Gut Project mapping file

description: The full American Gut Project mapping file, includes non-fecal samples.
DOI: 10.6084/m9.figshare.6137606
title: The impact of b-values on diffusion-weighted imaging radiomic features and a retrospective study to characterize the hepatic cirrhosis

description: DWI RADIOMICS OF HEPATIC CIRRHOSIS-PEERJ
DOI: 10.6084/m9.figshare.6138248
title: Additional file 3: of Favorable outcome of patients with lung adenocarcinoma harboring POLE mutations and expressing high PD-L1

description: Table S1. Descriptive characteristics of the POLE-mutant and -wild TCGA LUSC patients. Table S2 Descriptive characteristics of the POLE-mutant and -wild TCGA LUAD patients. Table S3. Descriptive characteristics of the Mut-High and -Low TCGA LUAD patients. Table S4. Descriptive characteristics of the Mut-High and -Low TCGA LUSC patients. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.6138248.v1
title: Additional file 3: of Favorable outcome of patients with lung adenocarcinoma harboring POLE mutations and expressing high PD-L1

description: Table S1. Descriptive characteristics of the POLE-mutant and -wild TCGA LUSC patients. Table S2 Descriptive characteristics of the POLE-mutant and -wild TCGA LUAD patients. Table S3. Descriptive characteristics of the Mut-High and -Low TCGA LUAD patients. Table S4. Descriptive characteristics of the Mut-High and -Low TCGA LUSC patients. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.6138272
title: Additional file 1: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

description: Config Example (YAML 6Â kb)
DOI: 10.6084/m9.figshare.6138272.v1
title: Additional file 1: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

description: Config Example (YAML 6Â kb)
DOI: 10.6084/m9.figshare.6138290
title: Additional file 2: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

description: Metasheet Example (CSV 600 bytes)
DOI: 10.6084/m9.figshare.6138290.v1
title: Additional file 2: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

description: Metasheet Example (CSV 600 bytes)
DOI: 10.6084/m9.figshare.6138326
title: MOESM1 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 1: Table S1. Primers used in qRT-PCR validation.
DOI: 10.6084/m9.figshare.6138326.v1
title: MOESM1 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 1: Table S1. Primers used in qRT-PCR validation.
DOI: 10.6084/m9.figshare.6138347
title: MOESM2 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 2: Table S2. Novel miRNAs identified in four life stages libraries of An. sinensis.
DOI: 10.6084/m9.figshare.6138347.v1
title: MOESM2 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 2: Table S2. Novel miRNAs identified in four life stages libraries of An. sinensis.
DOI: 10.6084/m9.figshare.6138353
title: Additional file 5: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

description: Complete VIPER report in html format (HTML 10310Â kb)
DOI: 10.6084/m9.figshare.6138353.v1
title: Additional file 5: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

description: Complete VIPER report in html format (HTML 10310Â kb)
DOI: 10.6084/m9.figshare.6138359
title: MOESM3 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 3: Table S3. Target gene candidates for known and novel miRNAs in An. sinensis.
DOI: 10.6084/m9.figshare.6138359.v1
title: MOESM3 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 3: Table S3. Target gene candidates for known and novel miRNAs in An. sinensis.
DOI: 10.6084/m9.figshare.6138374
title: MOESM4 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 4: Table S4. Developmental target gene candidates for 32 key miRNAs during development in An. sinensis.
DOI: 10.6084/m9.figshare.6138374.v1
title: MOESM4 of Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages

description: Additional file 4: Table S4. Developmental target gene candidates for 32 key miRNAs during development in An. sinensis.
DOI: 10.6084/m9.figshare.6142871
title: MOESM1 of Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)

description: Additional file 1. SHLCI 2010_2015. Information on cases assessed in the study of severe influenza laboratory confirmed hospitalized cases. Catalonia (Spain) from 2010–2011 to 2014–2015.
DOI: 10.6084/m9.figshare.6142871.v1
title: MOESM1 of Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)

description: Additional file 1. SHLCI 2010_2015. Information on cases assessed in the study of severe influenza laboratory confirmed hospitalized cases. Catalonia (Spain) from 2010–2011 to 2014–2015.
DOI: 10.6084/m9.figshare.6147188
title: Additional file 10: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S5B. Differential expression of DH2 vs YN2 greater than 2 (microarray). (XLSX 585Â kb)
DOI: 10.6084/m9.figshare.6147188.v1
title: Additional file 10: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S5B. Differential expression of DH2 vs YN2 greater than 2 (microarray). (XLSX 585Â kb)
DOI: 10.6084/m9.figshare.6147209
title: Additional file 11: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S6A. Differential expression of DH3 vs YN3 less than point 5 (microarray). (XLSX 512Â kb)
DOI: 10.6084/m9.figshare.6147209.v1
title: Additional file 11: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S6A. Differential expression of DH3 vs YN3 less than point 5 (microarray). (XLSX 512Â kb)
DOI: 10.6084/m9.figshare.6147230
title: Additional file 12: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S6B. Differential expression of DH3 vs YN3 greater than 2 (microarray). (XLSX 556Â kb)
DOI: 10.6084/m9.figshare.6147230.v1
title: Additional file 12: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S6B. Differential expression of DH3 vs YN3 greater than 2 (microarray). (XLSX 556Â kb)
DOI: 10.6084/m9.figshare.6147242
title: Additional file 12: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Markers used in this study. List of names of extracted FASTA sequences for SNP markers used to construct the genome (TXT 841Â kb)
DOI: 10.6084/m9.figshare.6147242.v1
title: Additional file 12: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Markers used in this study. List of names of extracted FASTA sequences for SNP markers used to construct the genome (TXT 841Â kb)
DOI: 10.6084/m9.figshare.6147266
title: Additional file 4: of Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

description: Table S1. Result of differential expression ananlysis on all genes in stomach, pyloric caeca and hindgut of 2.5 and 10 g salmon both compared to 0.16 g. (XLSX 14268 kb)
DOI: 10.6084/m9.figshare.6147266.v1
title: Additional file 4: of Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

description: Table S1. Result of differential expression ananlysis on all genes in stomach, pyloric caeca and hindgut of 2.5 and 10 g salmon both compared to 0.16 g. (XLSX 14268 kb)
DOI: 10.6084/m9.figshare.6147272
title: Additional file 13: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Comparison of Actinidia ESTâ s to manually annotated gene models.Summary of the raw results for the best BLAT gene set match protein of the sequenced cDNAs and manually annotated predicted peptides. (XLSX 102Â kb)
DOI: 10.6084/m9.figshare.6147272.v1
title: Additional file 13: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Comparison of Actinidia ESTâ s to manually annotated gene models.Summary of the raw results for the best BLAT gene set match protein of the sequenced cDNAs and manually annotated predicted peptides. (XLSX 102Â kb)
DOI: 10.6084/m9.figshare.6147281
title: Additional file 15: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S9. Ten categories of TFs with BN oligonucleotides retrieved from stem section comparisons of B. napus DH12075 (DH) and YN01â 429 (YN). (XLSX 100Â kb)
DOI: 10.6084/m9.figshare.6147281.v1
title: Additional file 15: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S9. Ten categories of TFs with BN oligonucleotides retrieved from stem section comparisons of B. napus DH12075 (DH) and YN01â 429 (YN). (XLSX 100Â kb)
DOI: 10.6084/m9.figshare.6147284
title: Additional file 5: of Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

description: Table S1. Result of KEGG ontology enrichment analysis on differential expressed genes (DEG) in stomach, pyloric caeca and hindgut of 0.16 and 2.5 g salmon both compared to 0.16 g. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.6147284.v1
title: Additional file 5: of Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

description: Table S1. Result of KEGG ontology enrichment analysis on differential expressed genes (DEG) in stomach, pyloric caeca and hindgut of 0.16 and 2.5 g salmon both compared to 0.16 g. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.6147290
title: Additional file 1: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Map back rates to the Red5 genome sequence.Summary of the numbers of input reads reads that align to the RED5 genome construction (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6147290.v1
title: Additional file 1: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Map back rates to the Red5 genome sequence.Summary of the numbers of input reads reads that align to the RED5 genome construction (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6147308
title: Additional file 2: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: BAC alignment to chromosome 25.Table summarising alignments of contigs from 22 BAC clones to chromosome 25 of the Red5 assembly (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6147308.v1
title: Additional file 2: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: BAC alignment to chromosome 25.Table summarising alignments of contigs from 22 BAC clones to chromosome 25 of the Red5 assembly (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6147314
title: Additional file 1: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S1A. Differential expression of DH1 vs DH4 less than point 5 (microarray). (XLSX 360Â kb)
DOI: 10.6084/m9.figshare.6147314.v1
title: Additional file 1: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S1A. Differential expression of DH1 vs DH4 less than point 5 (microarray). (XLSX 360Â kb)
DOI: 10.6084/m9.figshare.6147329
title: Additional file 2: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S1B. Differential expression of DH1 vs DH4 greater than 2 (microarray). (XLSX 442Â kb)
DOI: 10.6084/m9.figshare.6147329.v1
title: Additional file 2: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S1B. Differential expression of DH1 vs DH4 greater than 2 (microarray). (XLSX 442Â kb)
DOI: 10.6084/m9.figshare.6147347
title: Additional file 3: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S2A. Differential expression of DH1 vs YN1 less than point 5 (microarray). (XLSX 496Â kb)
DOI: 10.6084/m9.figshare.6147347.v1
title: Additional file 3: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S2A. Differential expression of DH1 vs YN1 less than point 5 (microarray). (XLSX 496Â kb)
DOI: 10.6084/m9.figshare.6147353
title: Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: BLASTP comparison of manually edited gene models to the revised ‘Hongyang’ gene models. List of best reciprocal BLASTp matches between the revised Actinidia chinensis ‘Hongyang’ genes [18]and the Red5 gene set (XLSX 436 kb)
DOI: 10.6084/m9.figshare.6147353.v1
title: Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: BLASTP comparison of manually edited gene models to the revised ‘Hongyang’ gene models. List of best reciprocal BLASTp matches between the revised Actinidia chinensis ‘Hongyang’ genes [18]and the Red5 gene set (XLSX 436 kb)
DOI: 10.6084/m9.figshare.6147365
title: Additional file 4: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S2B. Differential expression of DH1 vs YN1 greater than 2 (microarray). (XLSX 565Â kb)
DOI: 10.6084/m9.figshare.6147365.v1
title: Additional file 4: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S2B. Differential expression of DH1 vs YN1 greater than 2 (microarray). (XLSX 565Â kb)
DOI: 10.6084/m9.figshare.6147380
title: Additional file 5: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S3A. Differential expression of YN1 vs YN4 less than point 5 (microarray). (XLSX 226Â kb)
DOI: 10.6084/m9.figshare.6147380.v1
title: Additional file 5: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S3A. Differential expression of YN1 vs YN4 less than point 5 (microarray). (XLSX 226Â kb)
DOI: 10.6084/m9.figshare.6147386
title: Additional file 5: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: ‘Hongyang’ Gene models that align to Red5 genome.List of Actinidia chinensis ‘Hongyang’ genes that align to the Red5 whole genome sequence. Additional file 5A: models from original ‘Hongyang’ annotation [14]. Additional file 5B: models from revised ‘Hongyang’ annotation [18] (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6147386.v1
title: Additional file 5: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: ‘Hongyang’ Gene models that align to Red5 genome.List of Actinidia chinensis ‘Hongyang’ genes that align to the Red5 whole genome sequence. Additional file 5A: models from original ‘Hongyang’ annotation [14]. Additional file 5B: models from revised ‘Hongyang’ annotation [18] (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6147401
title: Additional file 6: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S3B. Differential expression of YN1 vs YN4 greater than 2 (microarray). (XLSX 417Â kb)
DOI: 10.6084/m9.figshare.6147401.v1
title: Additional file 6: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S3B. Differential expression of YN1 vs YN4 greater than 2 (microarray). (XLSX 417Â kb)
DOI: 10.6084/m9.figshare.6147410
title: Additional file 6: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Revised â Hongyangâ genes omitted from the manually edited gene set. Average RNA-Seq read coverage of the 1069 KIR V2 models perfectly aligned to the Red5 genome without a protein match in the Red5 gene set. (XLSX 114Â kb)
DOI: 10.6084/m9.figshare.6147410.v1
title: Additional file 6: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

description: Revised â Hongyangâ genes omitted from the manually edited gene set. Average RNA-Seq read coverage of the 1069 KIR V2 models perfectly aligned to the Red5 genome without a protein match in the Red5 gene set. (XLSX 114Â kb)
DOI: 10.6084/m9.figshare.6147416
title: Additional file 7: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S4A. Differential expression of DH4 vs YN4 less than point 5 (microarray). (XLSX 728Â kb)
DOI: 10.6084/m9.figshare.6147416.v1
title: Additional file 7: of Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

description: Table S4A. Differential expression of DH4 vs YN4 less than point 5 (microarray). (XLSX 728Â kb)