cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3639398_d4.v1
title: MOESM2 of Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs

description: Additional file 2. Inbreeding.example. This file contains a small dataset with information on ROH length for two individuals on chromosome 1. The variables are: nchro: number of chromosome; ind: number of individuals; gr: group; po1: initial chromosomal position; po2: final chromosomal position; roh: ROH length in number of homozygous SNPs in the segment.
DOI: 10.6084/m9.figshare.c.3639398_d5.v1
title: MOESM4 of Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs

description: Additional file 4. Quantile.r. Source code in R for estimating quantile inbreeding coefficients.
DOI: 10.6084/m9.figshare.c.3639506_d2.v1
title: Additional file 4: of Motif signatures in stretch enhancers are enriched for disease-associated genetic variants

description: De novo motif disocvery results. Zip archive of de novo motif discovery results. Discovered motifs are condensed in MEME Minimal Motif Format. TOMTOM output HTML files documenting the comparison of the discovered motifs to known motifs and CentriMo output text files detailing the enrichment of the discovered motifs in SE or TE DHS sequences are also included. File names indicate the type of sequences used for the motif discovery, including the method of footprinting. Can be downloaded at http://fusion.nhgri.nih.gov/files/se-motifs/AdditionalFile4.zip .
DOI: 10.6084/m9.figshare.c.3639506_d3.v1
title: Additional file 3: of Motif signatures in stretch enhancers are enriched for disease-associated genetic variants

description: CentriMo scans of DHS sequences with database motifs. Zip archive of text outputs from CentriMo scans on DHS sequences within SEs or TEs using database motifs. File names specify the cell type and enhancer class. Can be downloaded at http://fusion.nhgri.nih.gov/files/se-motifs/AdditionalFile3.zip .
DOI: 10.6084/m9.figshare.c.3639506_d4.v1
title: Additional file 1: of Motif signatures in stretch enhancers are enriched for disease-associated genetic variants

description: Table S1. Staitistics of enhancers.
DOI: 10.6084/m9.figshare.c.3606647_d6.v1
title: Additional file 5: of Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

description: The alignment used for the calculations of the double-domain sequences tree. (FASTA 53Â kb)
DOI: 10.6084/m9.figshare.c.3606647_d7.v1
title: Additional file 1: of Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

description: The alignment of GmrSD family members. (FASTA 6123Â kb)
DOI: 10.6084/m9.figshare.c.3606647_d8.v1
title: Additional file 8: of Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

description: Results of the genomic context analysis. (XLS 41Â kb)
DOI: 10.6084/m9.figshare.c.3639518_d1.v1
title: Additional file 1: of Association between genotypic diversity and biofilm production in group B Streptococcus

description: Strains examined in this study. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.c.3639701_d2.v1
title: Additional file 2: of 
                     TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

description: Reformatted file of â  gene variation IARC TP53 databaseâ   to use in Galaxy workflow for variants annotation. (TXT 1603 kb)
DOI: 10.6084/m9.figshare.c.3639950_d1.v1
title: Additional file 3: of Deep, multi-stage transcriptome of the schistosomiasis vector Biomphalaria glabrata provides platform for understanding molluscan disease-related pathways

description: KEGG annotations and pathway maps. (GZ 23266 kb)
DOI: 10.6084/m9.figshare.c.3639950_d2.v1
title: Additional file 2: of Deep, multi-stage transcriptome of the schistosomiasis vector Biomphalaria glabrata provides platform for understanding molluscan disease-related pathways

description: Annotations of transcriptome. (GZ 1986 kb)
DOI: 10.6084/m9.figshare.c.3639950_d3.v1
title: Additional file 4: of Deep, multi-stage transcriptome of the schistosomiasis vector Biomphalaria glabrata provides platform for understanding molluscan disease-related pathways

description: Sequences of all genes referred to in text. (XLSX 130 kb)
DOI: 10.6084/m9.figshare.c.3640136_d10.v1
title: Additional file 8: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: 65 candidate orthologs among the six genomes. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d11.v1
title: Additional file 9: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: 11 orthologs among the downy mildew genomes. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d12.v1
title: Additional file 17: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Cystatin-like domain features among the different genomes. (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d13.v1
title: Additional file 23: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Six orthologs of candidate RxLR-like proteins among the downy mildew genomes. (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d14.v1
title: Additional file 20: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Candidate RxLR-like effectors of Pl. halstedii, predictions based on gene models. (XLSX 98Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d17.v1
title: Additional file 6: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Five candidate orthologs among the nine genomes. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d18.v1
title: Additional file 21: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Candidate RxLR-like effectors of Pl. halstedii, predictions based on ORFs generated from the un-masked genome. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d19.v1
title: Additional file 26: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Gene expression values of down-regulated candidate RxLR-like proteins and CRNs of Pl. halstedii. (XLSX 65Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d21.v1
title: Additional file 7: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: 77 candidate orthologs among the five genomes. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d22.v1
title: Additional file 22: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Proteins with positive score for WY-fold hidden Markov model. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d25.v1
title: Additional file 11: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: PMSE gene ids of Pl. halstedii. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d23.v1
title: Additional file 25: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Gene expression values of up-regulated candidate RxLR-like proteins and CRNs of Pl. halstedii. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d24.v1
title: Additional file 3: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Simple sequence repeats within the genome of Plasmophara halstedii . (XLSX 26Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d26.v1
title: Additional file 24: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Three orthologs of candidate RxLR-like proteins among the downy mildew and Phytophthora spp. genomes. (XLSX 32Â kb)
DOI: 10.6084/m9.figshare.c.3640139_d2.v1
title: Additional file 29: of Ascertainment bias from imputation methods evaluation in wheat

description: Best linear unbiased predictors (BLUPs) for each genotype for spikes per square meter. (txt 9 kb)
DOI: 10.6084/m9.figshare.c.3640139_d5.v1
title: Additional file 26: of Ascertainment bias from imputation methods evaluation in wheat

description: Best linear unbiased predictors (BLUPs) for each genotype for plant height. (txt 9 kb)
DOI: 10.6084/m9.figshare.c.3640211_d2.v1
title: MOESM1 of Handling missing items in the Hospital Anxiety and Depression Scale (HADS): a simulation study

description: Additional file 1: Appendix S1. Individual results.
DOI: 10.6084/m9.figshare.c.3640220_d1.v1
title: Additional file 1: of A comprehensive and scalable database search system for metaproteomics

description: This file contains supplementary figures, methods, and four supplementary tables: Table S1. Data sources used for generation of ComPIL database. Table S2. Adenovirus 5 proteins identified by a ComPIL search of a human HEK293 sample. Table S3. List of proteomes used for generation of the â  46 proteomesâ   database. Table S4. Statistics summary of 3 technical replicates of 5 human fecal samples. (ZIP 1371Â kb)
DOI: 10.6084/m9.figshare.c.3640229_d1.v1
title: MOESM1 of Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression

description: Additional file 1: Table S1. List of differentially-expressed 2d pathways. The complete list of differentially-expressed 2d pathways that were identified by an adjusted p â ¤ 0.1. Table S2. List of differentially-expressed transcripts. Details of the transcripts identified as differentially expressed between wild and domesticated embryos. Table S3. Essential genes of the differentially-expressed pathways. Gene members of pathways that contribute most to their differential expression. Table S4. Key genes of the differentially-expressed pathways.
DOI: 10.6084/m9.figshare.c.3640256_d1.v1
title: Additional file 2: of Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia

description: The Matrix of data containing the list of SNPs selected after filtration crossed with selected samples. The â  Nâ   tags the individuals where alleles are missing from the sequence reads. This could either be as a result of lack of a read at this site or a poor quality sequence, which cannot be called. (TXT 2744Â kb)
DOI: 10.6084/m9.figshare.c.3640337_d1.v1
title: Additional file 9: of Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin

description: Annotated Results (Male cohort). Linear modeling was performed to identify differentially abundant transcripts between TCDD-treated and control samples. A total of 21,115 transcripts were assessed in this study. Transcripts were annotated with Entrez Gene ID, gene Symbol and chromosome. Coefficients representing log2 fold-change and FDR-adjusted p-values are given. (XLSX 3725Â kb)
DOI: 10.6084/m9.figshare.c.3640337_d2.v1
title: Additional file 6: of Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin

description: Sample Information. A total of 20 male and 20 female mice were included in this experiment. Each animal was treated with either corn oil or a single dose of TCDD (125, 250, 500 or 1000 μg/kg) dissolved in corn oil. Liver tissue was collected 4 days after treatment. (XLS 31 kb)
DOI: 10.6084/m9.figshare.c.3640337_d4.v1
title: Additional file 10: of Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin

description: Annotated Results (Female cohort). Linear modeling was performed to identify differentially abundant transcripts between TCDD-treated and control samples. A total of 21,115 transcripts were assessed in this study. Transcripts were annotated with Entrez Gene ID, gene Symbol and chromosome. Coefficients representing log2 fold-change and FDR-adjusted p-values are given. (XLSX 3730Â kb)
DOI: 10.6084/m9.figshare.c.3640337_d5.v1
title: Additional file 11: of Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin

description: Transcription Factor Binding Site Analysis. The count of occurrences and conservation scores for each of four AHRE motifs [AHRE-I (core), AHRE-I (extended), AHRE-I (full), and AHRE-II] were determined for each gene (within 3kbp up- and downstream of the transcription start site). For comparison, the number of doses at which each gene was altered by TCDD (p adj â
DOI: 10.6084/m9.figshare.c.3640337_d8.v1
title: Additional file 3: of Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin

description: Pathway Analysis. Pathway analysis was performed using GOMiner software to identify enriched gene ontologies within each sex/dose cohort. Enrichment scores and FDR-adjusted p-values are provided. (XLS 2546Â kb)
DOI: 10.6084/m9.figshare.c.3640349_d2.v1
title: Additional file 1: of The expanded program on immunization service delivery in the Dschang health district, west region of Cameroon: a cross sectional survey

description: Dataset. (XLSX 86.4 kb)
DOI: 10.15468/dl.wjhkzm
title: Occurrence Download

description: A dataset containing 1233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.74909 9.09246,-78.24205 6.84672,-77.96818 3.99846,-79.28276 2.24569,-79.33754 1.31452,-77.36567 -0.10961,-76.05109 -0.10961,-74.57218 -0.87644,-73.20283 -2.73877,-70.51889 -3.01264,-71.06663 -4.38199,-69.69728 -4.60109,-68.76612 -0.65735,-68.32792 1.75272,-66.6847 3.66981,-66.95857 6.40852,-69.58773 7.06582,-71.7787 7.44923,-72.54554 9.42111,-71.66915 11.28343,-70.73799 12.81711,-72.87418 13.2553,-77.74909 9.09246))",
 "TaxonKey is Nannotrigona Cockerell, 1922"
 ]
}

 The dataset includes 1233 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038062-241126133413365/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.3640433_d4.v1
title: Additional file 2: Table S1. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: (a) Positions and (b) C57Bl6/J-129S5/SvEvBrd SNP information for analyzed PE-4Cseq viewpoints on chromosome 4. Primers used for Sanger sequencing are shown. (XLSX 26Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d6.v1
title: Additional file 5: Table S4. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Unique (a) df and (b) Df/+â   D Bl6 regions. All chromosome 4 positions are shown. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d7.v1
title: Additional file 4: Table S3. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Summary of median magnitude of change, direction, and number of +  D Bl6 DIRs for viewpoints 1–12. Notice how only viewpoint 5 displays an increase in contact probabilities (63 % of total regions). Viewpoints 3, 4, and 9 show a ~50 % split between regions with an increase and decrease in contact probabilities, while the rest of the viewpoints show a variable range in the decrease in interactions (60–79 % of total regions per viewpoint). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3640433_d8.v1
title: Additional file 3: Table S2. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Summary of median magnitude of change, direction, and number of df DIRs for viewpoints 1, 2, 11, and 12. Notice how viewpoint 1 displays an increase in contact probabilities with surrounding sequences (64 % of total detected regions), while viewpoints 2 and 11 show mostly a decrease in interactions (60 % for viewpoint 2, and 95 % for viewpoint 11). Viewpoint 12 has both increase and decrease in interactions in approximately the same magnitude (~50 %). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3640433_d10.v1
title: Additional file 13: Table S12. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Candidate genes associated with different Monosomy 1p36 phenotypes. Their corresponding mouse homologues are shown in column 3, together with their chromosomal positions (columns 5,6). Their overlaps with df DIRs are displayed in columns 7–9, as well as the direction of change of the contact probabilities (1 = increase,–1 = decrease. Both compared to + 129 ). RNA-Seq derived expression in Df/+ Bl6 MEFs is shown in columns 11,12. Mouse gene coordinates are expressed in NCBI37/mm9 assembly, while human is GRCh38. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3640433_d9.v1
title: Additional file 9: Table S8. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Combined DE genes of three + 129 /+ Bl6 and four Df/+â   D Bl6 MEF revealed by RNA-Seq. (XLSX 170Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d12.v1
title: Additional file 12: Table S11. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: C57Bl6/J allele-specific DE genes of three + 129 /+ Bl6 and four Df/+â   D Bl6 MEF revealed by RNA-Seq. (XLSX 48Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d13.v1
title: Additional file 11: Table S10. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: 129S5/SvEvBrd allele-specific DE genes of three + 129 /+ Bl6 and four Df/+â   D Bl6 MEF revealed by RNA-Seq. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.c.3640439_d2.v1
title: MOESM2 of Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008

description: Additional file 2: List of all reactions contained in the network and the corresponding enzyme accession numbers.
DOI: 10.6084/m9.figshare.c.3640451_d2.v1
title: Additional file 4: Table S2. of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

description: Upregulated mutants upregulated mutant list and ko phenotype description. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.c.3640451_d4.v1
title: Additional file 1: Table S1. of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

description: Gene set: The genes identified and additional information on orthology, detection method, and expression peak. (XLSX 97Â kb)
DOI: 10.6084/m9.figshare.c.3640559_d1.v1
title: Additional file 2: of Towards the bridging of molecular genetics data across Xenopus species

description: Map of X. laevis, XLA9.1, 18 chromosomes on X. tropicalis , XTR9.0, 10 chromosomes. (XLSX 22301Â kb)
DOI: 10.6084/m9.figshare.c.3640559_d2.v1
title: Additional file 3: of Towards the bridging of molecular genetics data across Xenopus species

description: Annotation of biological function of transcripts of XLA9.1 and XTR9.0. (ZIP 29029Â kb)
DOI: 10.6084/m9.figshare.c.3640562_d1.v1
title: Additional file 2 of Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development

description: Table S2.1. List of all identified proteins. Table S2.2. Proteins with significantly changing abundance in the transition from cambium to phloem. Table S2.3. Proteins with significantly changing abundance in the transition from cambium to expansion zone. Table S2.4. Proteins with significantly changing abundance in the transition from expansion zone to xylemX1. Table S2.5. Proteins with significantly changing abundance in the transition from xylemX1 to xylemX2. Table S2.6. Proteins with significantly changing abundance in the transition from xylemX2 to xylemX3. Table S2.7. Proteins with significantly changing abundance in the transition from xylemX3 to xylemX4. Table S2.8. Subcellular localizations of proteins in the wood series analysis sorted by location designation. (XLSX 348 kb)
DOI: 10.6084/m9.figshare.c.3640562_d2.v1
title: Additional file 1: of Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development

description: Table S1.1. Anatomical characterization and pooling scheme for tree1. Table S1.2. Anatomical characterization and pooling scheme for tree2. Table S1.3. Anatomical characterization and pooling scheme for tree3. Table S1.4. Anatomical characterization and pooling scheme for tree4. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3640565_d1.v1
title: Additional file 9: Table S10. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Differential gene responses to CPA in GL261(scid) and GL261(B6) tumors. (XLSX 2296 kb)
DOI: 10.6084/m9.figshare.c.3640565_d2.v1
title: Additional file 7: Table S7. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Genes whose basal expression in untreated GL261(B6) tumors is either higher or lower than in untreated LLC and untreated B16F10 tumors. (XLSX 670 kb)
DOI: 10.6084/m9.figshare.c.3640565_d5.v1
title: Additional file 1: Table S1. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Significant gene responses induced by metronomic CPA treatment in each of the indicated tumor models. Shown in Tables S1A-S1F are genes differentially expressed between CPA-treated and control (drug-free) GL261(B6) tumors (Table S1A), LLC tumors (Table S1B), B16F10 tumors (Table S1C), and GL261(scid) tumors (Table S1D, following treatment with CPA/6d; Table S1E, treatment with CPA/9d; and Table S1F, genes common to CPA/6d and CPA/6d treatment). Treatments and other data about RNA-seq samples, including GSM accession numbers within GEO data set GSE71491, are also shown. (XLSX 3150 kb)
DOI: 10.6084/m9.figshare.c.3640565_d3.v1
title: Additional file 6: Table S5. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Negative regulators of immune response. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.c.3640565_d6.v1
title: Additional file 3: Table S2. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Listed are all CPA-induced upstream regulators (UPRs) as predicted by IPA for CPA-treated GL261(B6) (Table S2A), LLC (Table S2B), B16F10 (Table S2C), GL261(scid) (Table S2D; CPA/6d treatment), and GL261(scid) (Table S2E; CPA/9d treatment) tumors, respectively. (XLSX 960 kb)