cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3643277_d8
title: Additional file 6: Table S5. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: All differentially down-regulated genes during saprotrophic growth of R. microporus. (XLSX 1631Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d9
title: Additional file 13: Table S8. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: List of all differentially expressed ATPâ  Binding cassette (ABC) transporters. (XLSX 394Â kb)
DOI: 10.15468/dl.p6ca8c
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is Quercus sessiliflora Salisb. ex Sm., 1804"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034137-241126133413365/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.3643385_d1
title: Additional file 4: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Per strain genotype concordance with HapMap. Total HapMap positions available for comparison with each strain and the corresponding number of concordant sites. (XLSX 4 kb)
DOI: 10.6084/m9.figshare.c.3643385_d2
title: Additional file 3: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Pairwise variant comparisons. The number of SNPs and indels shared between any two strains contained in the MGP variation catalogue. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3643385_d3
title: Additional file 5: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: VEP, GMS and SIFT annotations for SNPs and indels in each of the 13 strains. Total number of SNPs and indels annotated into each functional consequence predicted by VEP. Total number of SNPs with an estimated moderate (using GMS), radical (GMS), tolerated (using SIFT) and deleterious (SIFT) effect is also provided. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3643385_d5
title: Additional file 7: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Candidate genes identified in the RF/J analysis. All genes which contained at least one missense SNP only found in the RF/J strain. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3643385_d7
title: Additional file 6: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Private SNPs with multiple VEP consequences. Private SNPs with multiple predicted VEP consequences for each strain strain. Consequence predictions are based on gene models obtained from Ensembl 78. (TXT 66669 kb)
DOI: 10.6084/m9.figshare.c.3643385_d8
title: Additional file 8: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Per strain over-represented pathways using genes containing private missense SNPs. For each strain separately significantly over-represented pathways were identified using only the genes which contained at least one private missense variant. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.c.3643445_d1
title: Additional file 3: Table S3. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

description: WebGestalt Disease enrichment analysis of the set of unique DEX-regulated genes (n = 139) with TSS near epigenetic clock CpGs. For the primary analysis, we used as reference the set of genes expressed above background in our peripheral blood gene expression arrays. This analysis was repeated using a more condensed background comprised only of the genes neighboring 21 K CpGs that showed DEX-induced mRNA expression changes (n = 5,443). While this post-hoc analysis yielded no statistically significant results after correction for multiple testing (P values presented in the last column), the top 10 diseases were very similar (with higher but nominally significant P values for the top three hits) with the analysis using the broader reference set of genes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3643445_d3
title: Additional file 1: Table S1. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

description: Location of epigenetic clock CpGs in relation to the nearest glucocorticoid response element (as shown by within GR ChIP-Seq peaks in a lymphoblastoid cell line) and their methylation changes in response to the glucocorticoid receptor agonist dexamethasone. (DEX). (XLSX 68 kb)
DOI: 10.6084/m9.figshare.c.3643445_d2
title: Additional file 2: Table S2. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

description: Annotation of genes with transcription start sites (TSS) near epigenetic clock CpGs and their expression changes in response to DEX. Gene annotation was based on [43]. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3643451_d1
title: Additional file 2: Table S2. of A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax)

description: Detailed positions of individual SNPs in the constructed genetic map. (CSV 281 kb)
DOI: 10.6084/m9.figshare.c.3643451_d2
title: Additional file 1: Table S1. of A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax)

description: Origin of samples and barcodes. This file provides details for each sample used i.e., sample ID, family, gender, barcode used, number of raw reads paired-ended and number of RAD-tags. (CSV 23 kb)
DOI: 10.6084/m9.figshare.c.3643472_d1
title: Additional file 1 of Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

description: Table with expression fold changes and p-values. Excel file with all expression FPKM values for all genes, fold changes and FDR corrected p-values for all genes that were found to be significantly differentially expressed in at least one comparison. The file also includes the assignments of genes to expression biclusters. (XLS 19558 kb)
DOI: 10.6084/m9.figshare.c.3643469_d1
title: Additional file 1: of Pharmacokinetics (PK), pharmacodynamics (PD), and PK-PD integration of ceftiofur after a single intravenous, subcutaneous and subcutaneous-LA administration in lactating goats

description: Plasma Ceftiofur concentrations and time kill curves data. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3643475_d2
title: Additional file 1: of Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells

description: A Microsoft Excel file that contains spreadsheets of Caco-2 genes differentially expressed in response to B. infantis grown on GLU, LAC, or HMO. (XLSX 86 kb)
DOI: 10.6084/m9.figshare.c.3643475_d1
title: Additional file 2: of Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells

description: A Microsoft Excel file that contains spreadsheets of Caco-2 genes differentially expressed in response to B. breve grown on GLU, LAC, or HMO. (XLSX 177 kb)
DOI: 10.6084/m9.figshare.c.3643550_d9
title: Additional file 4: Table S3. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Consensus genetic map (positions and RAD locus sequences). (CSV 235Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d11
title: Additional file 8: Table S5. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Male only genetic map (positions and RAD locus sequences). (CSV 130Â kb)
DOI: 10.6084/m9.figshare.c.3643565_d1
title: MOESM2 of Optimized methods for extracting circulating small RNAs from long-term stored equine samples

description: Additional file 2. Serum RNA extraction results from 120 samples. A table in XLSX format with serum absorbances at 414Â nm, serum volume used, sample collection year, and RNA concentrations obtained using the optimized procedures and measured with Qubit and Bioanalyzer.
DOI: 10.6084/m9.figshare.c.3643565_d2
title: MOESM3 of Optimized methods for extracting circulating small RNAs from long-term stored equine samples

description: Additional file 3. RNA extraction from EDTA. A table in XLSX format with RNA concentration and yield measured with Qubit, miRNA concentration measured with Bioanalyzer, and RNA quality number (RQN) measured by Fragment Analyzer in samples used for pilot experiments during method optimization and with already optimized method.
DOI: 10.6084/m9.figshare.c.3643565_d3
title: MOESM1 of Optimized methods for extracting circulating small RNAs from long-term stored equine samples

description: Additional file 1. RNA extraction from serum. A table in XLSX format with RNA concentration and yield measured with Qubit, miRNA concentration and rRNA contamination measured with Bioanalyzer in samples used for pilot experiments during method optimization. Read numbers of the six samples sequenced are also given.
DOI: 10.6084/m9.figshare.c.3643574_d3
title: Additional file 10: Table S5. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Presents the gene expressionÂ in our datasets of a number of previously known AD disease genes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3643574_d4
title: Additional file 5: Figure S3. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Downregulated genes in AD Br5â  6. The input genes Additional file 8: Table S4) are bioinformatically translated to proteins and the symbols are colored. Another set of genes/proteins is inserted by the knowledgedatabase to construct the most likely networks; the symbols are white. Different types of symbols exist (for explanation see www.ingenuity.com : transporters, strucural proteins, secreted proteins, etc). The symbols are connected by solid lines and dotted lines. These denote, respectively, direct physical/functional and indirect interaction between the symbols/genes/proteins. These interactions are, via the knowledgde database, derived form wet lab experiments in the literature, and from big data stored in curated public databases (GEO, etc). The most likely networks are constructed by the knowledge database, taken all available data into account of human, mouse, rat and in vitro model experiments. Finally, once the networks are constructed, specific entries in the networks can be labelled, by hand of the user, to specifically label molecules wihch are involved in sopecific diseases or biological process of interest. In this way, the (predicted) molecular enviroment of entries of interest can be explored. (ZIP 10804 kb)
DOI: 10.6084/m9.figshare.c.3643574_d5
title: Additional file 6: Table S3. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains the specifications of genes upregulated in CPE Br(5â  6) compared to CPE Br(0,1). (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3643574_d7
title: Additional file 3: Table S2. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains compilations of lists of (disease) genes previously implicated in relevant disease. The entries are used to label the molecular network in Additional file 4: Figure S2Â and Additional file 5: Figure S3. (XLS 190 kb)
DOI: 10.6084/m9.figshare.c.3643574_d8
title: Additional file 8: Table S4. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains the specifications of genes downregulated in CPE Br(5â  6) compared to CPE Br(0,1). (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3643574_d10
title: Additional file 1: Tabel S1. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains characteristics of donor eyes used. (XLS 25 kb)
DOI: 10.6084/m9.figshare.c.3643577_d1
title: Additional file 1: of 
                     Dirofilaria infections in dogs in different areas of Greece

description: Data collected from the questionnaires filled in for each examined dog. (XLSX 91Â kb)
DOI: 10.6084/m9.figshare.c.3643583_d1
title: Additional file 10: Table S5. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Detailed information on CRISPR/Cas9 cleavage efficiency studies. Number of guides, cell types, delivery, and expression method of the guide RNA and comments. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3643793_d9
title: Additional file 13: Table S5. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Expression of transposable element (TE) related genes. (XLSX 45Â kb) (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d12
title: Additional file 22: Table S12. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Commonly detected changed-tissues jiDE genes between the NM and NZ combinations. (XLSX 53Â kb) (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d14
title: Additional file 8: Table S4. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Molecular evolution of jiDE genes. (XLSX 61Â kb) (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d15
title: Additional file 23: Table S13. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Details of expression quantitative trait loci (eQTLs) detected global Minghui63-Zhenshan97 differentially expressed (MZDE) genes. (XLSX 45Â kb) (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d16
title: Additional file 24: Table S14. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Details of expression quantitative trait loci (eQTLs) detected changed-tissues Minghui63-Zhenshan97 differentially expressed (MZDE) genes. (XLSX 127Â kb) (XLSX 121Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d18
title: Additional file 15: Table S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: GO enrichment analysis of global jiDE genes of the NM combination. (XLSX 57Â kb) (XLSX 52Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d20
title: Additional file 17: Table S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NM combination. (XLSX 49Â kb) (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d22
title: Additional file 5: Table S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Highly expressed genes and the two types of jiDE genes of the two japonica-indica combinations in the five tissues. (XLSX 53Â kb) (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d23
title: Additional file 2: Table S1. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Rice gene expression data sets. (XLSX 70Â kb) (XLSX 66Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d26
title: Additional file 20: Table S11. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Expression types of global DE genes among the three strains. (XLSX 49Â kb) (XLSX 45Â kb)
DOI: 10.15468/dl.eby8j3
title: Occurrence Download

description: A dataset containing 13071 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xyleborus monographus (J.C.Fabricius, 1792)"
 ]
}

 The dataset includes 13071 records from 247 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034138-241126133413365/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.3643904_d16
title: Additional file 15: Table S11. of Mining kidney toxicogenomic data by using gene co-expression modules

description: List of chemical exposures modulating the expression of immunoproteasomes in kidney. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3643916_d1
title: Additional file 1: of A loss-of-function and H2B-Venus transcriptional reporter allele for Gata6 in mice

description: Figure 2 raw data. (CSV 163Â kb)
DOI: 10.6084/m9.figshare.c.3643922_d2
title: Additional file 1: Table S1. of Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

description: Summary data of 91 single-cell mouse T-cell RNAseq samples. Provided as a separate Excel file. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3643922_d1
title: Additional file 3: Table S3. of Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

description: Results of scTCRseq and VIDJIL run on simulated scRNAseq data at different read lengths and coverage. Provided as a separate Excel file. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3643919_d1
title: Additional file 1: of A review of policy dissemination and implementation research funded by the National Institutes of Health, 2007â  2014

description: NIH-funded policy D&I projects. (XLSM 583Â kb)
DOI: 10.6084/m9.figshare.c.3643922_d3
title: Additional file 5: Table S5. of Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

description: Summary of recovered alpha and beta chains in 71 selected single-cell mouse T-cell RNAseq samples. Provided as a separate Excel file. Samples with multiple productive alpha or beta chain sequences highlighted in yellow. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.c.3643922_d4
title: Additional file 4: Table S4. of Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

description: Raw counts of reads mapping to TRA and TRB variable gene loci in 71 selected single-cell mouse T-cell RNAseq samples. Provided as a separate Excel file. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.c.3643922_d5
title: Additional file 2: Table S2. of Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

description: Results of scTCRseq and VIDJIL run on three replicate Jurkat T-cell RNAseq samples. Provided as a separate Excel file. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3643928_d2
title: Additional file 1: Table S1. of Distribution of Îą-synuclein in the spinal cord and dorsal root ganglia in an autopsy cohort of elderly persons

description: Clinicopathological characteristics of 265 subjects with LBAS. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3643934_d1
title: Additional file 1: of Birth weight-for-gestational age is associated with DNA methylation at birth and in childhood

description: Descriptive characteristics of methylation levels in birth weight-for-gestational age (BW/GA)-associated DNA methylation sites in venous umbilical cord blood at delivery, among 476 participants in Project Viva. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3643946_d2
title: Additional file 13: Dataset S1. of The Drosophila transcriptional network is structured by microbiota

description: Read counts per gene. Each column denotes a different sample. See Table S4 for line name information. Samples suffixed by “a” are axenic, samples suffixed by “g” are gnotobiotic. Reads aligning to genomic regions coding for multiple genes are tabulated to a feature representing the multiple possible genes. (CSV 2506 kb)
DOI: 10.6084/m9.figshare.c.3643946_d3
title: Additional file 9: Table S5. of The Drosophila transcriptional network is structured by microbiota

description: GO enrichment amongst microbiota-dependent transcriptional modules. Enrichment of GO terms in microbiota-dependent modules was analyzed in Cytoscape using BINGO. The table shows transcriptional module identifiers, description of GO terms enriched (FDR ≤ 0.05) in each module, the GO term identifiers, and p-values (FDR). (CSV 31 kb)
DOI: 10.6084/m9.figshare.c.3644135_d1
title: Additional file 1: of Comparative genomics of European avian pathogenic E. Coli (APEC)

description: Assembly statistics. (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.c.3644135_d2
title: Additional file 2: of Comparative genomics of European avian pathogenic E. Coli (APEC)

description: Cumulative table. (XLSX 87Â kb)
DOI: 10.6084/m9.figshare.c.3644135_d3
title: Additional file 3: of Comparative genomics of European avian pathogenic E. Coli (APEC)

description: Hits. (XLSX 2118Â kb)
DOI: 10.6084/m9.figshare.c.3644144_d1
title: MOESM4 of Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr

description: Additional file 4: Table S4. Transcription factor enrichment analysis using WEB-based GEne SeT AnaLysis Toolkit (WebGestalt v2). The list of more than 200 genes co-expressed with Chd4, Cspp1 and Dlg1 in human and mice are used as input. (Cut-off criteria: p
DOI: 10.6084/m9.figshare.c.3644144_d2
title: MOESM3 of Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr

description: Additional file 3: Table S3. Chd4-Cspp1-Dlg1 co-expressed genes in humans and mice retrieved from COXPRESdb. More than 200 genes were identified to have co-expression with Chd4, Cspp1 and Dlg1 after setting the mutual rank (MR) to the top-ranked 2000 genes and the reliability score of 1 to 3.
DOI: 10.6084/m9.figshare.c.3644144_d3
title: MOESM2 of Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr

description: Additional file 2: Table S2. Primers designed for cDNA cloning and qPCR study of Arctic charr.
DOI: 10.6084/m9.figshare.c.3644234_d6
title: Additional file 7: Table S5. of Lactation undernutrition leads to multigenerational molecular programming of hypothalamic gene networks controlling reproduction

description: Canonical pathways identified by Ingenuity Pathway Analysis for genes showing differential expression in the hypothalamus of control (CON) vs. LUN mice. Significance for the enrichment of the genes within a particular Canonical pathway was determined by Fisher's exact test right-tailed using the whole database as a reference set (Th = −log(p-value) = 1.3). (XLSX 18 kb)