cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3597884_d8
title: Additional file 7: of Initiator tRNA genes template the 3′ CCA end at high frequencies in bacteria

description: TFAM model used to reannotate tRNA functions in COVE format. To use this model file with TFAM, give its name as an option argument to the “-m” option. (TXT 1 MB)
DOI: 10.6084/m9.figshare.c.3597884_d9
title: Additional file 3: of Initiator tRNA genes template the 3â ˛ CCA end at high frequencies in bacteria

description: Expanded description of each additional file with usage. (TXT 3 kb)
DOI: 10.6084/m9.figshare.c.3597884_d10
title: Additional file 12: of Initiator tRNA genes template the 3â ˛ CCA end at high frequencies in bacteria

description: Web-browser based navigator of full dataset of results on frequencies of CCA-templating by tRNA functional class, organized by clades in NCBI taxonomy. (ZIP 548 kb)
DOI: 10.6084/m9.figshare.c.3598022_d13
title: Additional file 10: Model S10. of Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders

description: Human-liver fatty acid beta-oxidation no competition. (XML 233Â kb)
DOI: 10.6084/m9.figshare.c.3598052_d1
title: Additional file 3: Table S2. of DAPPER: a data-mining resource for protein-protein interactions

description: List of unique CGIDs in DAPPER. Uniprot ID is shown where CGID was not available. (XLSX 92Â kb)
DOI: 10.6084/m9.figshare.c.3598052_d2
title: Additional file 2: Table S1. of DAPPER: a data-mining resource for protein-protein interactions

description: List of unique Baits in DAPPER. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.28012703.v1
title: Gene annotation, protein models, coding sequences list for stinging nettle female (<i>Urtica dioica</i> ssp. <i>dioica</i>)

description: Gene annotation of Nettle female (<i>Urtica dioica</i> ssp. <i>dioica</i>) genome using BRAKER3. The .tar.gz file contains the following 6 files:Gene annotation of haplotype 1 in .gtf (braker3.Nettle_female_H1_v2_RNA_ProtsViridiplantaeOrthoDB.gtf)Gene annotation of haplotype 2 in .gtf (braker3.Nettle_female_H2_v2_RNA_ProtsViridiplantaeOrthoDB.gtf)List of protein sequences annotated in haplotype 1 in amino acid .fasta format (braker3.Nettle_female_H1_v2_RNA_ProtsViridiplantaeOrthoDB.faa)List of protein sequences annotated in haplotype 2 in amino acid .fasta format (braker3.Nettle_female_H2_v2_RNA_ProtsViridiplantaeOrthoDB.faa)List of coding sequences (CDS) annotated in haplotype 1 in nucleotide .fasta format (braker3.Nettle_female_H1_v2_RNA_ProtsViridiplantaeOrthoDB.codingseq)List of protein sequences (CDS) annotated in haplotype 2 in nucleotide .fasta format (braker3.Nettle_female_H2_v2_RNA_ProtsViridiplantaeOrthoDB.codingseq)Note that headers of the protein sequences match the "transcript" IDs on the .gtf file, meaning the protein sequences include all the splicing variants predicted.
DOI: 10.6084/m9.figshare.c.3598079_d1
title: Additional file 1: of Health-related quality of life in stroke patients questionnaire, short version (HRQOLISP-40): validation for its use in Colombia

description: Data base HRQOLISP-40 Colombia. Description of data: Acces date base. (ACCDB 1828 kb)
DOI: 10.6084/m9.figshare.c.3598112_d6
title: Additional file 7: of Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains

description: Quantitative 3C dataset for WT mouse embryonic stem cells. (XLS 89Â kb)
DOI: 10.6084/m9.figshare.c.3598127_d1
title: Additional file 1: of Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease

description: Microbiome samples sequencing and analysis summary. Contains a table that summarizes total reads, reads passing QC, and reads successfully classified under closed and de novo OTU-picking approaches for each sample. Also provided are the dysbiosis and Shannon index values for samples under the aforementioned approaches along with median values after 10,000 rarefactions (subsamplings) of the closed-reference.biom table. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3598112_d7
title: Additional file 6: of Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains

description: Quantitative 3C primer sequences. (XLS 56Â kb)
DOI: 10.6084/m9.figshare.c.3598088_d15
title: Additional file 2: of Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

description: SNPs with Bonferroni corrected p-values higher than 0.05 (−log10(p) ≥ 8.50) for the fat yield. Columns on table: SNP = marker name, CHR, position on bp, alleles, Beta = variation effect, SE = standard error for effect, P = p-value, minuslog10 = (−log10(p)-values), Bonferroni corrected p-value. For the rest of the columns, see explanation from http://www.ensembl.org/common/Help/Glossary?db=core . (XLSX 859 kb)
DOI: 10.6084/m9.figshare.c.3598127_d3
title: Additional file 3: of Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease

description: De novo and rarefy analysis. Contains a table that compares results from the generalized estimating equation (GEE) analysis performed in the paper (using closed-reference OTU picking) to de novo OTU picking and rarefied closed-reference approaches. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3598136_d1
title: Additional file 5: of Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae

description: Results correlation analysis phosphomutants within one condition. (XLSX 70Â kb)
DOI: 10.6084/m9.figshare.c.3598136_d2
title: Additional file 3: of Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae

description: Results on growth rates and maximal cell densities from growth experiments. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.c.3598136_d3
title: Additional file 8: of Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae

description: Corrected p-values from untargeted metabolomics. (XLSX 1258Â kb)
DOI: 10.6084/m9.figshare.28012793.v1
title: Transposable elements annotation for stinging nettle female (<i>Urtica dioica </i>ssp. <i>dioica</i>)

description: Transposable elements (TEs) annotation of Nettle female (<i>Urtica dioica</i> ssp. <i>dioica</i>) genome using EDTA. The .tar.gz file contains the following 8 files:TE annotation of haplotype 1 chromosomes in .gff3 (Nettle_female_H1.chr.fa.mod.EDTA.TEanno.gff3)TE annotation of haplotype 2 chromosomes in .gff3 (Nettle_female_H2.chr.fa.mod.EDTA.TEanno.gff3)TE annotation of haplotype 1 non-chromosomal contigs in .gff3 (Nettle_female_H1_non_chr_scaff.fa.mod.EDTA.TEanno.gff3)TE annotation of haplotype 2 non-chromosomal contigs in .gff3 (Nettle_female_H2_non_chr_scaff.fa.mod.EDTA.TEanno.gff3)TE annotation of haplotype 1 chromosomes in .bed (Nettle_female_H1.chr.fa.mod.EDTA.TEanno.bed)TE annotation of haplotype 2 chromosomes in .bed (Nettle_female_H2.chr.fa.mod.EDTA.TEanno.bed)TE annotation of haplotype 1 non-chromosomal contigs in .bed (Nettle_female_H1_non_chr_scaff.fa.mod.EDTA.TEanno.bed)TE annotation of haplotype 2 non-chromosomal contigs in .bed (Nettle_female_H2_non_chr_scaff.fa.mod.EDTA.TEanno.bed)
DOI: 10.6084/m9.figshare.c.3598088_d18
title: Additional file 3: of Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

description: SNPs with Bonferroni corrected p-values higher than 0.05 (−log10(p) ≥ 8.50) for the milk yield. Columns on table: SNP = marker name, CHR, position on bp, alleles, Beta = variation effect, SE = standard error for effect, P = p-value, minuslog10 = (−log10(p)-values), Bonferroni corrected p-value. For the rest of the columns, see explanation from http://www.ensembl.org/common/Help/Glossary?db=core . (XLSX 209 kb)
DOI: 10.6084/m9.figshare.c.3598256_d1
title: Additional file 2: of Exploration of alternative splicing events in ten different grapevine cultivars

description: Table with all AS predicted by FindAS software. First row (beginning with '#') hold the column labels. (ZIP 1893 kb)
DOI: 10.6084/m9.figshare.c.3598358_d5
title: Additional file 1 of De novo transcriptome reconstruction and annotation of the Egyptian rousette bat

description: Gene Ontology analysis of all tissues. Three sheets contain enriched GO terms of Biological Process, Molecular Function, and Cellular Compartment in individual tissues. (XLS 31 kb)
DOI: 10.6084/m9.figshare.c.3598325_d8
title: Additional file 4: of Monoamine oxidase B gene variants associated with attention deficit hyperactivity disorder in the Indo-Caucasoid population from West Bengal

description: Population-based comparative analysis on allelic frequencies of MAOB variants. Description: The table summarizes allelic frequencies of MAOB variants in ADHD cases and ethnically matched controls. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3598325_d9
title: Additional file 2: of Monoamine oxidase B gene variants associated with attention deficit hyperactivity disorder in the Indo-Caucasoid population from West Bengal

description: Protocol followed for analysis of MAOB target regions. Description: The table summarizes the protocol followed for analysis of target sites. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3598346_d12
title: Additional file 12 of Changes in correlation between promoter methylation and gene expression in cancer

description: Top genes regulated by methylation for breast normal tissues, lung normal and cancerous tissues and colon cancerous tissues. (CSV 3.48 kb)
DOI: 10.6084/m9.figshare.c.3598394_d1
title: Additional file 2: of Serum depletion induces changes in protein expression in the trophoblast-derived cell line HTR-8/SVneo

description: Table S3. DIGE analysis: proteins identified via MS and bioinformatics analysis from 0.5 % serum culture. HTR-8/SVneo cells were grown in medium with 10 or 0.5 % FBS for 24 h. Total protein extracts (40 μg) were labeled with either Cy2 or Cy3 and analyzed using 2D–DIGE technology in triplicate, as previously described. Protein spots were analyzed via MALDI TOF and identified using the MASCOT search engine. MW (kDa) – theoretical and experimental molecular weight in kDalton; pI ~ – theoretical pI; MS score – protein score given by Mascot; % Seq – percentage sequence coverage; Pep match – number of peptides assigned to protein; Fold FBS 0.5 %/10 % – fold optical density of protein spot (expression) of 0.5 % serum proteomes (0.5 % FBS) compared to control proteomes (10 % FBS). Relevant GO terms for molecular function and biological process, retrieved by Nextprot database and DAVID tool. (XLS 90 kb)
DOI: 10.15468/dl.vnejtf
title: Occurrence Download

description: A dataset containing 236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sonora aemula (Cope, 1879)"
 ]
}

 The dataset includes 236 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032645-241126133413365/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.3598448_d5
title: Additional file 13 of Multicopy gene family evolution on primate Y chromosomes

description: DAZ maximum clade credibility tree. Summary of 95 % high posterior density interval information for tree shown in Additional file 1: Figure S2. (TREE 48.5 KB)
DOI: 10.6084/m9.figshare.c.3598496_d1
title: Additional file 2 of Smear positivity in paediatric and adult tuberculosis: systematic review and meta-analysis

description: Table of additional details for included studies. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.c.3598448_d6
title: Additional file 10 of Multicopy gene family evolution on primate Y chromosomes

description: XKRY BEAST input file. Alignment, calibration nodes, nucleotide substitution model, and specification of priors for tree shown in Additional file 1: Figure S7. (XML 33 kb)
DOI: 10.6084/m9.figshare.c.3598433_d10
title: Additional file 7: of Engineering high Zn in tomato shoots through expression of AtHMA4 involves tissue-specific modification of endogenous genes

description: Microarray data. (XLSX 2637 kb)
DOI: 10.5281/zenodo.13858468
title: Sediment thickness of the USA from seismic receiver functions

description: Data relating to the results of "Sediment thickness of the contiguous United States from seismic receiver functions" (submitted).

 

Summary dataset of sediment thicknesses measured at seismic stations across the USA.  Original reciever functions obtained from the IRIS EARS database.  The data is provided in two formats, simple txt and geojson.  Both files contain the same data.  For each station, the receiver function delay time (in seconds) and two estimates of sediment thickness (in kilometres) are given.

UPDATE v2: The addition of further stations from the BK network in California's Central Valley
DOI: 10.5281/zenodo.13858469
title: Sediment thickness of the USA from seismic receiver functions

description: Data relating to the results of "Sediment thickness of the contiguous United States from seismic receiver functions" (submitted).

 

Summary dataset of sediment thicknesses measured at seismic stations across the USA.  Original reciever functions obtained from the IRIS EARS database.  The data is provided in two formats, simple txt and geojson.  Both files contain the same data.  For each station, the receiver function delay time (in seconds) and two estimates of sediment thickness (in kilometres) are given.
DOI: 10.5281/zenodo.14429658
title: Sediment thickness of the USA from seismic receiver functions

description: Data relating to the results of "Sediment thickness of the contiguous United States from seismic receiver functions" (submitted).

 

Summary dataset of sediment thicknesses measured at seismic stations across the USA.  Original reciever functions obtained from the IRIS EARS database.  The data is provided in two formats, simple txt and geojson.  Both files contain the same data.  For each station, the receiver function delay time (in seconds) and two estimates of sediment thickness (in kilometres) are given.

UPDATE v2: The addition of further stations from the BK network in California's Central Valley
DOI: 10.6084/m9.figshare.c.3598448_d7
title: Additional file 19 of Multicopy gene family evolution on primate Y chromosomes

description: XKRY maximum clade credibility tree. Summary of 95 % high posterior density interval information for tree shown in Additional file 1: Figure S7. (TREE 52.4 KB)
DOI: 10.6084/m9.figshare.c.3598448_d8
title: Additional file 4 of Multicopy gene family evolution on primate Y chromosomes

description: DAZ BEAST input file. Alignment, calibration nodes, nucleotide substitution model, and specification of priors for tree shown in Additional file 1: Figure S2. (XML 139 kb)
DOI: 10.6084/m9.figshare.c.3598448_d9
title: Additional file 2 of Multicopy gene family evolution on primate Y chromosomes

description: Nine concatenated msrY-linked singleton genes BEAST input file. Alignment, calibration nodes, nucleotide substitution model, and specification of priors for tree shown in Fig. 1. (XML 129 kb)
DOI: 10.6084/m9.figshare.c.3598448_d10
title: Additional file 3 of Multicopy gene family evolution on primate Y chromosomes

description: CDY BEAST input file. Alignment, calibration nodes, nucleotide substitution model, and specification of priors for tree shown in Additional file 1: Figure S1. (XML 101 kb)
DOI: 10.6084/m9.figshare.c.3598448_d11
title: Additional file 16 of Multicopy gene family evolution on primate Y chromosomes

description: TSPY maximum clade credibility tree. Summary of 95 % high posterior density interval information for tree shown in Additional file 1: Figure S5. (TREE 106 KB)
DOI: 10.6084/m9.figshare.c.3598634_d1
title: MOESM1 of Insecticide resistance profile of Anopheles gambiae from a phase II field station in CovĂŠ, southern Benin: implications for the evaluation of novel vector control products

description: Additional file 1. Full microarray results.
DOI: 10.6084/m9.figshare.c.3598610_d5
title: Additional file 1: of Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2

description: Segregation data for markers in L. angustifolius linkage groups NLL-10 and NLL-17. (XLS 132 kb)
DOI: 10.6084/m9.figshare.c.3598610_d6
title: Additional file 9: of Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2

description: Substitution rates, selective pressure and estimated divergence time of PEBP-family genes in legumes. (XLS 56 kb)
DOI: 10.6084/m9.figshare.c.3598610_d7
title: Additional file 8: of Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2

description: PEBP-family reference sequences and homologs identified in the genomes of ten legume species. (XLS 74 kb)
DOI: 10.6084/m9.figshare.c.3598610_d8
title: Additional file 4: of Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2

description: Transcriptome sequences assigned to genes predicted in superscaffolds carrying LanFTc1 and LanFTc2 genes. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3598610_d10
title: Additional file 6: of Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2

description: Microsyntenic links identified between superscaffold-2 and legume genome regions. Sequences producing numerous links dispersed over many chromosomes were denoted as “repetitive”. (XLS 259 kb)
DOI: 10.6084/m9.figshare.c.3598772_d1
title: Additional file 1: of Investigation of Streptococcus salivarius-mediated inhibition of pneumococcal adherence to pharyngeal epithelial cells

description: Supporting Information S1. Raw data used to generate figures and tables. (XLSX 52Â kb)
DOI: 10.6084/m9.figshare.c.3598781_d3
title: Additional file 13 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

description: Data set S1. SNP positions and genotype calls. This additional data set contains SNP positions relative to the published draft genome [30]. The first column identifies the scaffold containing the SNP. The value after the final underscore identifies the SNP position within this scaffold. The second column identifies the alleles, and the remaining columns are the genotype calls for each individual. NN refers to a missing genotype. (ZIP 6379 kb)
DOI: 10.6084/m9.figshare.c.3598796_d1
title: Additional file 6: of Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network

description: GWAS datasets were used for hypothesis-driven gene set analysis. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.c.3598802_d2
title: Additional file 2: of Systematic review on the evaluation criteria of orphan medicines in Central and Eastern European countries

description: Contains the extracted dataset which summarizes the general characteristics of the included articles and type of articles. Furthermore, separate columns summarizes the main findings of the articles referring to the specific elements of HTA, as well as other factors to consider in terms of public reimbursement. (XLSX 86 kb)
DOI: 10.6084/m9.figshare.c.3598859_d5
title: Additional file 4: Dataset S1. of Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family

description: Details and sequences of R-gene identified in each species. Grape (Vv): Vitis vinifera; Cultivated soybean (Gm): Glycine max; Wild soybean (Gs): Glycine soja; Barrel clover (Mt): Medicago truncatula; Birdâ  s-foot trefoil (Lj): Lotus japonicas; Pigeonpea (Cc): Cajanus cajan; Chickpea (Ca): Cicer arietinum; Common bean (Pv): Phaseolus vulgaris. (XLSX 1716 kb)
DOI: 10.6084/m9.figshare.c.3598859_d7
title: Additional file 1: Table S1. of Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family

description: Overview information of the seven published genomes in the legume family. Table S2. The genome assembly and number of identified R-genes in the seven legume species and grape. Table S3. The number of R-genes in each R-gene family in seven species of legumes and grape. Each row represents one R-gene family. Table S4. Global statistics of R-genes in families or clusters in seven species of legumes and grape. Table S5. Statistics on the expansions and contractions of R-genes during the evolution of legumes. Table S6. The gene pairs with outlier Ka/Ks values between wild and cultivated soybeans. The threshold for an outlier Ka/Ks value was set at 0.8. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3598889_d2
title: Additional file 3: Table S3. of Triatomine bugs, their microbiota and Trypanosoma cruzi: asymmetric responses of bacteria to an infected blood meal

description: Bacterial OTU identification and coverage. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3598889_d3
title: Additional file 2: Table S2. of Triatomine bugs, their microbiota and Trypanosoma cruzi: asymmetric responses of bacteria to an infected blood meal

description: Triatomine sample information. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3598976_d2
title: Additional file 10: of Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress

description: Primer sequences for selected variants to be used in building of integrated database. (XLSX 5540 kb)
DOI: 10.6084/m9.figshare.c.3598976_d3
title: Additional file 1: of Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress

description: Differentially expressed genes/transcripts in at least one sample with 2 fold change and at p-value of 0.001. (XLSX 162 kb)
DOI: 10.6084/m9.figshare.c.3599075_d2
title: Additional file 3 of Adaptive designs undertaken in clinical research: a review of registered clinical trials

description: Case studies. XLSX file containing a list of the trials used in the review. Trial number, title and URL are provided. (XLSX 35.2 kb)
DOI: 10.6084/m9.figshare.c.3599093_d1
title: Additional file 3: of Gene expression comparison of resistant and susceptible Atlantic salmon fry challenged with Infectious Pancreatic Necrosis virus reveals a marked contrast in immune response

description: Enriched KEGG pathways in all comparisons. List of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in all comparisons. KEGG pathway description, KEGG pathway ID, number of differentially expressed genes assigned to the corresponding KEGG pathway and their microarray IDs, number of genes assigned to the corresponding KEGG pathway in the whole microarray, false discovery rate corrected p-value and hyperlink to a visual representation of the KEGG pathway with the differentially expressed genes outlined are shown. (XLSX 92Â kb)
DOI: 10.6084/m9.figshare.c.3599045_d7
title: Additional file 4: Table S1. of Muscleblind-like 1 is required for normal heart valve development in vivo

description: Epithelial to Mesenchymal Transition RT2 Profiler PCR Array data for Mbnl1 ∆E3/∆E3 versus wild type E10.5 AVC cushions. (XLS 42 kb)