cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3901453_d1.v1
title: Additional file 1: Table S1. of Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction

description: Core genes of 12 Citrobacter sp. (XLS 3788 kb)
DOI: 10.6084/m9.figshare.c.3901453_d1
title: Additional file 1: Table S1. of Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction

description: Core genes of 12 Citrobacter sp. (XLS 3788 kb)
DOI: 10.6084/m9.figshare.c.3901453_d2.v1
title: Additional file 2: Table S2. of Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction

description: C. werkmanii BF-6 strain specific genes. (XLS 52 kb)
DOI: 10.6084/m9.figshare.c.3901459_d1.v1
title: Additional file 1: Table S1. of Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract

description: E. coli strains included in this study (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3901453_d2
title: Additional file 2: Table S2. of Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction

description: C. werkmanii BF-6 strain specific genes. (XLS 52 kb)
DOI: 10.6084/m9.figshare.c.3901459_d1
title: Additional file 1: Table S1. of Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract

description: E. coli strains included in this study (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3901459_d2.v1
title: Additional file 2: Table S2. of Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract

description: Genes encoding virulence factors in the E. coli BG1 genome (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.c.3903664_d11
title: Additional file 1: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

description: Summary of RNA-Seq reads generated per sample and mapping statistics. Number of raw sequenced reads, high quality reads and mapped reads for each analyzed sample. Multi-mapped reads mapping on more than 10 different positions (MAPQÂ =Â 0) were filtered out and library statistics after filtering are reported too. R1 and R2 indicate replicate 1 and 2, respectively. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3903664_d11.v1
title: Additional file 1: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

description: Summary of RNA-Seq reads generated per sample and mapping statistics. Number of raw sequenced reads, high quality reads and mapped reads for each analyzed sample. Multi-mapped reads mapping on more than 10 different positions (MAPQÂ =Â 0) were filtered out and library statistics after filtering are reported too. R1 and R2 indicate replicate 1 and 2, respectively. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3903691_d2.v1
title: Additional file 2: of Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

description: Molecular basis of African yam domestication: analyses of selection point to starch biosynthesis, root development and photosynthesis related genes. Table S1. Passport data of plant material collected from Benin. Table S2. Metric information of data filtering and mapping. Table S3. Mean Nucleotide diversity (π) and polymorphism (ɵ). Table S4. List of the contigs detected as selected by at least one method. Table S5. Remarkable candidate genes showing selection signature. Table S6. Gene Ontology (GO) terms significantly enriched (p-value ≤ 0.05) among the 998 candidate contigs. Table S7. Gene Ontology (GO) terms significantly enriched (p-value ≤ 0.05) among the 81 candidates contigs detected by a least two methods. Figure S1. Cross-entropy calculated using sNMF (Frichot et al., 2014) for K = 1 to 6. Ten repetitions of the run were done. Figure S2. Intra-contigs linkage disequilibrium (LD) as a function of physical distance between SNPs pairs from 1% of all contigs. Figure S3. Venn Diagram comparing the candidate contigs obtained using the 4 methods. Figure S4. Distribution of Tajima’s D value calculated for D. abyssinica (a) and D. praehensilis (b). Figure S5. Comparison of diversity lost. Figure S6. Variance explained by PCA axis (a) and distribution of Mahalanobis distance (b) from PCAdapt. Figure S7. Nucleotide diversity within five candidate contigs for cultivated and the wild species (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3903691_d2
title: Additional file 2: of Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

description: Molecular basis of African yam domestication: analyses of selection point to starch biosynthesis, root development and photosynthesis related genes. Table S1. Passport data of plant material collected from Benin. Table S2. Metric information of data filtering and mapping. Table S3. Mean Nucleotide diversity (π) and polymorphism (ɵ). Table S4. List of the contigs detected as selected by at least one method. Table S5. Remarkable candidate genes showing selection signature. Table S6. Gene Ontology (GO) terms significantly enriched (p-value ≤ 0.05) among the 998 candidate contigs. Table S7. Gene Ontology (GO) terms significantly enriched (p-value ≤ 0.05) among the 81 candidates contigs detected by a least two methods. Figure S1. Cross-entropy calculated using sNMF (Frichot et al., 2014) for K = 1 to 6. Ten repetitions of the run were done. Figure S2. Intra-contigs linkage disequilibrium (LD) as a function of physical distance between SNPs pairs from 1% of all contigs. Figure S3. Venn Diagram comparing the candidate contigs obtained using the 4 methods. Figure S4. Distribution of Tajima’s D value calculated for D. abyssinica (a) and D. praehensilis (b). Figure S5. Comparison of diversity lost. Figure S6. Variance explained by PCA axis (a) and distribution of Mahalanobis distance (b) from PCAdapt. Figure S7. Nucleotide diversity within five candidate contigs for cultivated and the wild species (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3905881_d2
title: Additional file 2: of 
                     Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures

description: Shows the correspondence of each Dm28c Supra Gene to CL Brener Esmeraldo haplotype ID here used to compare the present work with that of Li and collaborators [44]. (XLSX 589Â kb)
DOI: 10.6084/m9.figshare.c.3905881_d3
title: Additional file 3: of 
                     Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures

description: Summary of all samples analyzed in present work containing results of RNA-Seq alignments and SRA accession IDs. (XLS 24 kb)
DOI: 10.6084/m9.figshare.c.3905947_d1.v1
title: Additional file 1: of Effectiveness and safety of dipeptidyl peptidase 4 inhibitors in the management of type 2 diabetes in older adults: a systematic review and development of recommendations to reduce inappropriate prescribing

description: Excluded studies. List of excluded studies after full-text check with reasons for exclusion. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.c.3907060_d8
title: MOESM8 of Metabolic responses to ethanol and butanol in Chlamydomonas reinhardtii

description: Additional file 8: Table S7. Primer pairs used in qRT-PCR analysis.
DOI: 10.6084/m9.figshare.c.3907072_d9.v1
title: Additional file 9: of Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

description: The best fitting substitution models and number of meta-partitions for supermatrix A (domain-based) and supermatrix B (gene-based) according to PartitionFinder. (XLSX 5 kb)
DOI: 10.6084/m9.figshare.c.3907102_d1.v1
title: Additional file 10: of Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

description: File S5. Matrix of species-level counts, by sample. (XLSX 761Â kb)
DOI: 10.6084/m9.figshare.c.3907072_d9
title: Additional file 9: of Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

description: The best fitting substitution models and number of meta-partitions for supermatrix A (domain-based) and supermatrix B (gene-based) according to PartitionFinder. (XLSX 5 kb)
DOI: 10.6084/m9.figshare.c.3907102_d1
title: Additional file 10: of Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

description: File S5. Matrix of species-level counts, by sample. (XLSX 761Â kb)
DOI: 10.15468/dl.wrg8cf
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "OccurrenceStatus is Present",
 "TaxonKey is Elephas Linnaeus, 1758"
 ]
}

 The dataset includes 132 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040492-241126133413365/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.3907153_d7
title: Additional file 6: Table S4. of Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication

description: Conservation of genes (lrig1 - thoc7) around rho among vertebrates. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3909646_d2.v1
title: Additional file 2: of Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening

description: Context sequences for AXIOM markers. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3909646_d3.v1
title: Additional file 3: of Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening

description: Genetic maps built on XRQxPSC8 and FUxPAZ2 RIL populations from a framework consensus genetic map. (XLSX 122 kb)
DOI: 10.15468/dl.2nmgfg
title: Occurrence Download

description: A dataset containing 124752 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Desmognathus Baird, 1850)"
 ]
}

 The dataset includes 124752 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040490-241126133413365/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.3909646_d3
title: Additional file 3: of Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening

description: Genetic maps built on XRQxPSC8 and FUxPAZ2 RIL populations from a framework consensus genetic map. (XLSX 122 kb)
DOI: 10.6084/m9.figshare.c.3909646_d2
title: Additional file 2: of Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening

description: Context sequences for AXIOM markers. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3909661_d2.v1
title: Additional file 2: of Characterizing the transcriptome and microsatellite markers for almond (Amygdalus communis L.) using the Illumina sequencing platform

description: Frequency distribution of SSRs from different motif types. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3911671_d1
title: MOESM1 of Genome-wide profiling of transcribed enhancers during macrophage activation

description: Additional file 1: Table S1. 184 macrophage samples used in this study. Table S2. 744 FANTOM5 non-macrophage mouse samples that were used as a background set for the calculation of macrophage-specific expression. Table S3. Established regulatory associations between transcribed enhancers, promoters and protein-coding genes. Table S4. Gene set enrichment analysis of 1306 genes associated with three or four enhancers. Table S5. Gene set enrichment analysis of 4149 genes not associated with any enhancer. Table S6. Gene set enrichment analysis of top 500 genes with the highest expression in macrophages among 1481 genes associated with macrophage-specific enhancers. Table S7. Gene set enrichment analysis of top 500 genes with the highest expression in macrophages among 1207 genes associated with non-macrophage-specific enhancers. Table S8. Regulatory associations between 115 M(IFN-γ)-responsive enhancers and 105 M(IFN-γ)-responsive genes. Table S9. Regulatory associations between 131 M(IL-4/IL-13)-responsive enhancers and 98 M(IL-4/IL-13)-responsive genes. Table S10. Over-representation analysis of binding sites in macrophage-specific and non-macrophage-specific enhancers. Table S11. Over-representation analysis of binding sites in E1 and E2 enhancers.
DOI: 10.6084/m9.figshare.c.3911671_d2.v1
title: MOESM2 of Genome-wide profiling of transcribed enhancers during macrophage activation

description: Additional file 2: Table S12. Numbers of overlapping regions between the CAGE-based enhancers and classes of ChIP-seq-based enhancers. Table S13. A matrix that shows whether each CAGE-based transcribed macrophage enhancer overlaps (value of 1) or does not overlap (value of 0) ChIP-seq-based enhancers of different classes.
DOI: 10.6084/m9.figshare.c.3911671_d2
title: MOESM2 of Genome-wide profiling of transcribed enhancers during macrophage activation

description: Additional file 2: Table S12. Numbers of overlapping regions between the CAGE-based enhancers and classes of ChIP-seq-based enhancers. Table S13. A matrix that shows whether each CAGE-based transcribed macrophage enhancer overlaps (value of 1) or does not overlap (value of 0) ChIP-seq-based enhancers of different classes.
DOI: 10.6084/m9.figshare.c.3911680_d1
title: MOESM1 of Sporadic PCDH18 somatic mutations in EpCAM-positive hepatocellular carcinoma

description: Additional file 1. Validated nonsynonymous somatic mutations.
DOI: 10.6084/m9.figshare.c.3911677_d2.v1
title: Additional file 2: of Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling

description: Table S1. Log ratios and p-values from DESeq analysis of read counts. Table S2. Genes and lncRNAs expressed at a higher level in aerial cells. Table S3. Genes and lncRNAs expressed at a higher level in roots. Table S4. S. cerevisiae orthologs of C. albicans secreted proteins. Table S5. Mapping and relative expression of lncRNA to lncRNA loci in GTF file. Table S6. All lncRNAs upregulated 2-fold in aerial or root and lying within 1.5 kB of a coding gene. Table S7. Yeast strains used in this study. Table S8. Primers and plasmids used in this study. (XLSX 2047 kb)
DOI: 10.6084/m9.figshare.c.3911677_d2
title: Additional file 2: of Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling

description: Table S1. Log ratios and p-values from DESeq analysis of read counts. Table S2. Genes and lncRNAs expressed at a higher level in aerial cells. Table S3. Genes and lncRNAs expressed at a higher level in roots. Table S4. S. cerevisiae orthologs of C. albicans secreted proteins. Table S5. Mapping and relative expression of lncRNA to lncRNA loci in GTF file. Table S6. All lncRNAs upregulated 2-fold in aerial or root and lying within 1.5 kB of a coding gene. Table S7. Yeast strains used in this study. Table S8. Primers and plasmids used in this study. (XLSX 2047 kb)
DOI: 10.6084/m9.figshare.c.3911686_d3.v1
title: Additional file 3: of Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification

description: Ocean acidification differential expression gene list. This file provides the list of all genes identified in the ocean acidification differential gene expression analysis. File contains, sequence identifier, sequence description, enzyme codes, gene ontology identifiers, gene ontology names, logFC (Fold Change), logCPM (Counts per million), P-values, and FDR (false discovery rate). (XLSX 741Â kb)
DOI: 10.6084/m9.figshare.c.3911680_d2.v1
title: MOESM2 of Sporadic PCDH18 somatic mutations in EpCAM-positive hepatocellular carcinoma

description: Additional file 2. The number of point mutations in 300 liver cancers and the function of 13 novel mutated genes.
DOI: 10.6084/m9.figshare.c.3911686_d2.v1
title: Additional file 2: of Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification

description: Seasonal differential expression gene list. This file provides the list of all genes identified in the seasonal differential gene expression analysis. File contains, sequence identifier, sequence description, enzyme codes, gene ontology identifiers, gene ontology names, logFC (Fold Change), logCPM (Counts per million), P-values, and FDR (false discovery rate). (XLSX 322Â kb)
DOI: 10.6084/m9.figshare.c.3911680_d2
title: MOESM2 of Sporadic PCDH18 somatic mutations in EpCAM-positive hepatocellular carcinoma

description: Additional file 2. The number of point mutations in 300 liver cancers and the function of 13 novel mutated genes.
DOI: 10.6084/m9.figshare.c.3911716_d4
title: Additional file 1: Table S1. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

description: Primers used for qRT-PCR analysis. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3913741_d12.v1
title: Additional file 5: Table S5. of Microbial biodiversity assessment of the European Space Agencyâ  s ExoMars 2016 mission

description: Sampling locations for molecular analyses (wipe samples). (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3913741_d11
title: Additional file 4: Table S4. of Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission

description: Biodiversity assay (“alternative assays”): Number of colony forming units (CFUs) per m^2. Numbers have been corrected by pour fraction and wipe efficiency (see Additional file 1: Table S1). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3913741_d12
title: Additional file 5: Table S5. of Microbial biodiversity assessment of the European Space Agencyâ  s ExoMars 2016 mission

description: Sampling locations for molecular analyses (wipe samples). (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3913741_d14.v1
title: Additional file 7: Table S7. of Microbial biodiversity assessment of the European Space Agencyâ  s ExoMars 2016 mission

description: Txt formatted biom table of Sanger sequencing data. (TXT 15Â kb)
DOI: 10.6084/m9.figshare.c.3913741_d13.v1
title: Additional file 6: Table S6. of Microbial biodiversity assessment of the European Space Agencyâ  s ExoMars 2016 mission

description: Txt formatted biom table of MiSeq amplicon data. (TXT 102Â kb)
DOI: 10.6084/m9.figshare.c.3913741_d13
title: Additional file 6: Table S6. of Microbial biodiversity assessment of the European Space Agencyâ  s ExoMars 2016 mission

description: Txt formatted biom table of MiSeq amplicon data. (TXT 102Â kb)
DOI: 10.6084/m9.figshare.c.3913741_d14
title: Additional file 7: Table S7. of Microbial biodiversity assessment of the European Space Agencyâ  s ExoMars 2016 mission

description: Txt formatted biom table of Sanger sequencing data. (TXT 15Â kb)
DOI: 10.6084/m9.figshare.c.3913735_d4.v1
title: Additional file 4 of McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

description: TF motifs enriched in predicted DHSs. This table shows enriched PWMs in predicted DHSs for each cluster using the AME motif enrichment algorithm. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3913741_d16.v1
title: Additional file 9: Table S8. of Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission

description: Retrieved microbial isolates, the sampling date, location and enrichment strategy (“Fungi” refers to PD agar, see materials and methods). (XLSX 30 kb)
DOI: 10.6084/m9.figshare.c.3913735_d4
title: Additional file 4 of McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

description: TF motifs enriched in predicted DHSs. This table shows enriched PWMs in predicted DHSs for each cluster using the AME motif enrichment algorithm. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3916012_d1.v1
title: Additional file 1: Table S1. of Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome—from days to weeks

description: Table report the fast sequence of each OTU. Table S2. Metaproteomic dataset. A) Table report a summary of information on the peptides/proteins identified. B) Table include further insights on peptide identification and their implication in protein IDs inference. Table S3. Glycosyl hydrolase and glycosyl transferase production. A) Panel reports the identified GHs and GTs. The relative abundance (%) is detailed for each GH and GT family in each adaptation period. B) Panel shows the relative contribution (%) of the bacterial specimens encoding for the major GH and GT families identified over the three adaptation periods. C) Panel report the list of proteins classified in each of the identified GH and GT, along with the LFQ index and the relative bacterial families. Table S4. SCFA concentration. Table of the total SCFA, acetate, propionate and butyrate concentration of all animals at days 3 and 32. (ZIP 108295 kb)
DOI: 10.6084/m9.figshare.c.3916012_d1
title: Additional file 1: Table S1. of Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome—from days to weeks

description: Table report the fast sequence of each OTU. Table S2. Metaproteomic dataset. A) Table report a summary of information on the peptides/proteins identified. B) Table include further insights on peptide identification and their implication in protein IDs inference. Table S3. Glycosyl hydrolase and glycosyl transferase production. A) Panel reports the identified GHs and GTs. The relative abundance (%) is detailed for each GH and GT family in each adaptation period. B) Panel shows the relative contribution (%) of the bacterial specimens encoding for the major GH and GT families identified over the three adaptation periods. C) Panel report the list of proteins classified in each of the identified GH and GT, along with the LFQ index and the relative bacterial families. Table S4. SCFA concentration. Table of the total SCFA, acetate, propionate and butyrate concentration of all animals at days 3 and 32. (ZIP 108295 kb)
DOI: 10.5281/zenodo.10797569
title: The experimental results of assimilating SST, T-S profiles, and SSS data in the data assimilation system using ensemble adjustment Kalman filters in the CESM

description: [Related manuscript]

Qi Wang, Zheqi Shen, Yihao Chen, Xingrong Chen and Yunfei Zhang, Improving ocean analyses in the ensemble-based data assimilation system using the community earth system model by assimilating satellite sea surface salinity, submitted to Journal of Operational Oceanography.