cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3637691_d1.v1
title: Additional file 1: of Spontaneous phenotypic suppression of GacA-defective Vibrio fischeri is achieved via mutation of csrA and ihfA

description: The predicted mutations in VCW2E2 when Aligned to ES114 reference strain. Predicted mutation of strain VCW2E2 compared to the reference identified as genomic position by sequence ID and nucleotide position, followed by the nucleotide change, annotation of allele variation and gene and gene description of gene affected. Evidence of ancestral allele, if applicable, is provided by a list of the top Basic Local Alignment Search Tool results [49] to the allele variant. If no evidence exists, a description of whether the allele was confirmed as mutated or not confirmed is provided. Primers along with annealing temperatures and elongation times for Sanger re-sequencing of the alleles are listed. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3637697_d1.v1
title: Additional file 3: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Differentially expressed genes in DCIS.COM and SUM225 mouse intraductal xenograft model (MIND) xenografts during transition from 2 to 6 weeks. Significance analysis for microarrays (SAM) software was utilized to determine differentially expressed genes between the 2- to 6-week time point in both DCIS.COM and SUM225 cell lines. The cutoff for significance was determined by &lt;5 % false discovery rate. Two-class unpaired SAM analysis generated a list of significant genes and fold-change values between 2 and 6 weeks in DCIS.COM (18,590 downregulated; 10,227 upregulated) and SUM225 (19,953 downregulated and 14,691 upregulated). (XLSX 3297 kb)
DOI: 10.6084/m9.figshare.c.3637697_d4.v1
title: Additional file 4: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Wnt-pathway-specific genes differentially expressed in ductal carcinoma in situ DCIS.COM and SUM225 mouse intraductal xenograft model (MIND) xenografts during transition from 2 to 6 weeks. Genes significantly differentially expressed between the 2- to 6-week time point in both DCIS.COM and SUM225 cell lines were further analyzed using Ingenuity Pathway AnalysisÂŽ (IPA). The Wnt/Î˛-catenin canonical pathway was identified as a significantly upregulated pathway in both cell line MIND xenografts during transition from 2 to 6 weeks. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3637697_d9.v1
title: Additional file 10: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Analysis of The Cancer Genome Atlas (TCGA) data showing canonical Wnt pathways genes expressed in BCL9-high versus BCL9-low tumors. TCGA breast cancer samples with BCL9 levels above the range defined by normal samples were labeled upregulated in cancer (414 samples). The significant differentially expressed genes from TCGA analysis of BCL9-high versus BCL9-low tumors were analyzed in Ingenuity Pathway Analysis (IPA) and the canonical pathways with a p value â ¤0.05 were obtained. (XLS 124 kb)
DOI: 10.6084/m9.figshare.c.3637697_d10.v1
title: Additional file 11: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Analysis of the The Cancer Genome Atlas (TCGA) data showed differentially expressed genes in BCL9-high versus BCl9-low tumors. Differential gene expression was performed between TCGA breast cancer samples with a normal range of BCL9 and samples with upregulated BCL9. A list of significant genes (1,756 down regulated 980 upregulated) was obtained with a threshold of a false discovery rate â Ľ0.05 and log fold change 0.26. (XLSX 1492 kb)
DOI: 10.6084/m9.figshare.27872528
title: CCR2 KO Glioblastoma scRNAseq

description: Preprocessed and annotated scRNA-seq Seurat object of CCR2 KO dataset from mouse glioblastoma immune cells. Cell-type annotations have been preserved from the original study [GSE163120].
DOI: 10.6084/m9.figshare.c.3637700_d5.v1
title: Additional file 8: of Comparative transcriptome analysis of lufenuron-resistant and susceptible strains of Spodoptera frugiperda (Lepidoptera: Noctuidae)

description: Differentially expressed transcripts between resistant and susceptible strains of S. frugiperda to lufenuron. (XLS 95Â kb)
DOI: 10.6084/m9.figshare.c.3637985_d2.v1
title: Additional file 6: Table S4. of Seasonal immunoregulation in a naturally-occurring vertebrate

description: Gene Set Enrichment Analysis (GSEA) of RNAseq data with genes ranked by confounder-adjusted seasonal expression. (XLS 65Â kb)
DOI: 10.6084/m9.figshare.c.3637985_d6.v1
title: Additional file 2: Table S2. of Seasonal immunoregulation in a naturally-occurring vertebrate

description: Based on genome-wide (RNAseq) expression data, here we provide lists of seasonally-biased KEGG and REACTOME gene sets as determined by Gene Set Enrichment Analysis (GSEA). (XLS 64Â kb)
DOI: 10.6084/m9.figshare.c.3637985_d5.v1
title: Additional file 7: Table S5. of Seasonal immunoregulation in a naturally-occurring vertebrate

description: List of core seasonally-biased immune genes determined from RNAseq data. To populate this list, seasonally-biased ImmPort list genes were individually assessed for their immunological significance. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3637985_d7.v1
title: Additional file 1: Table S1. of Seasonal immunoregulation in a naturally-occurring vertebrate

description: Based on genome-wide (RNAseq) expression data, here we provide lists of annotated winter-biased and summer-biased genes, as defined by synchronous season-specific expression across study sites. (XLS 593Â kb)
DOI: 10.6084/m9.figshare.c.3637985_d8.v1
title: Additional file 3: Table S3. of Seasonal immunoregulation in a naturally-occurring vertebrate

description: Details of the selected gene sets used to probe winter- and summer-biased gene lists and/or gene modules from network analyses. (XLS 98Â kb)
DOI: 10.6084/m9.figshare.c.3638495_d2.v1
title: Additional file 3: Table S3. of Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes

description: Orthologous clusters. List of predicted orthologous clusters utilized to generate heat maps. (XLSX 667 kb)
DOI: 10.6084/m9.figshare.c.3638495_d4.v1
title: Additional file 2: Table S2. of Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes

description: Candidate OMPs from various Borrelia genomes. List of proteins predicted to be OMPs for all genomes analyzed. (XLS 311 kb)
DOI: 10.6084/m9.figshare.c.3638495_d3.v1
title: Additional file 1: Table S1. of Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes

description: Predictions for all ORFs. Lipoprotein, trans-membrane Îą-helix, cellular localization, and Î˛-barrel prediction data collected for all ORFs for all genomes analyzed. (XLS 5022 kb)
DOI: 10.6084/m9.figshare.c.3638843_d1.v1
title: Additional file 1: Text S1. of Spatial modeling of HIV and HSV-2 among women in Kenya with spatially varying coefficients

description: R-INLA codes used in the analysis. (R 12 kb)
DOI: 10.6084/m9.figshare.c.3638867_d2.v1
title: Additional file 2: Table S1b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: Standalone blast of H. indica IJ transcripts against H. bacteriophora genome. (XLSX 336 kb)
DOI: 10.6084/m9.figshare.c.3638867_d3.v1
title: Additional file 4: Table S3. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: KEGG Pathways represented by transcripts with FPKM value of â Ľ100 and â Ľ1000. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3638867_d5.v1
title: Additional file 1: Table S1a. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: Blast, KOG and PRK analysis of the H. indica IJ transcripts. (XLSX 2073 kb)
DOI: 10.6084/m9.figshare.c.3638867_d4.v1
title: Additional file 10: Table S7. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: RNAi effector pathway genes in H. indica. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3638867_d6.v1
title: Additional file 6: Table S5a. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: H. indica secretome prediction by SignalP. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.c.3638867_d8.v1
title: Additional file 5: Table S4. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: C. elegans kinase Group/family/subfamily not found in H. indica. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3638867_d7.v1
title: Additional file 12: of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: H. indica assembled sequences. (TXT 14804 kb)
DOI: 10.6084/m9.figshare.c.3638867_d12.v1
title: Additional file 7: Table S5b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: MEROPS analysis of H. indica transcripts to identify secreted peptidases, proteases, and peptides. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3638867_d9.v1
title: Additional file 11: Table S8. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: Orthologs of members of C. elegans gene classes present in H. indica at â Ľ25% identity and query coverage. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3638867_d11.v1
title: Additional file 9: Table S6b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: SSR type and microsatellites present in H. indica. (XLSX 187 kb)
DOI: 10.6084/m9.figshare.c.3638867_d10.v1
title: Additional file 3: Table S2. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

description: Transcript abundance of H. Indica transcripts along with KOG analysis of transcripts showing FPKM values ≥ 100 and ≥ 1000. (XLSX 486 kb)
DOI: 10.15468/dl.ux8szk
title: Occurrence Download

description: A dataset containing 1710 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-141.21360 10.82233,-52.78640 10.82233,-52.78640 46.17767,-141.21360 46.17767,-141.21360 10.82233))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Euphorbia antisyphilitica Zucc."
 ]
}

 The dataset includes 1710 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038060-241126133413365/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.3639053_d1.v1
title: Additional file 3: of Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network

description: Gene expression cuffdiff output (gene_exp.diff) using Nasonia transcriptome annotation 1.2. This supplemented the main result given in Additional file 2, due to some discrepancies between the two annotations. See sections Vâ  VI for how this result was produced. (XLSX 138 kb)
DOI: 10.6084/m9.figshare.c.3639053_d2.v1
title: Additional file 6: of Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network

description: Dorsoventrally regulated genes in Drosophila melanogaster. Column A: CG number corresponding to each gene. When available, CG is also a hyperlink to the corresponding BDGP page where in situ images can be found. Column B: Gene name. Column C: Gene symbol. Column D: Primary localization of RNA transcript at stage 4–6, determined from in situ data. Column E: Molecular function category determined from experimental data collected by flybase.org. Column F: Detection of Nasonia ortholog in RNAi-RNAseq differential expression data [No = not significant, − = no ortholog to detect, toll vs. dpp = significant differential expression between dorsalized and ventralized embryos, wt vs. dpp = significant differential expression between dorsalized and wt embryos, wt vs. toll = significant differential expression between ventralized and wt embryos]. Column G: Corresponding Nasonia vitripennis orthologs as reported by flybase.org [N/A = no known ortholog]. Column H: Novelty status of Drosophila genes for genes without Nasonia orthologs. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3639053_d3.v1
title: Additional file 4: of Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network

description: Annotation of all genes where significant differential expression (DE) was detected in at least one comparison. Each gene has two rows: one for the Toll vs. wt comparison, and one for the BMP(dpp) vs. wt. All data is from the annotation 2.0 file regardless of whether DE was detected only in the annotation 1.2 analysis. Columns B–H are essential information from the gene_exp.diff file. Column I = pattern of DE of the gene; Column J = primary embryonic expression pattern; Column K = any additional patterns of expression; Column L = general molecule type; Column M = whether gene has clear orthologs in flies, insects, other animals, or is novel; Column N = association with a signaling pathway; Column O = cell biological function of gene; Column P = fly ortholog (if applicable); Column Q = whether gene is expressed in a similar pattern in Drosophila. (XLSX 158 kb)
DOI: 10.6084/m9.figshare.c.3639053_d4.v1
title: Additional file 2: of Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network

description: Gene expression cuffdiff output (gene_exp.diff) using Nasonia transcriptome annotation 2.0. This result was used as the main basis for choosing genes to further validate with in situ hybridization. See sections Iâ  IV of the Additional file 1: Methods for how this result was produced. (XLSX 6260 kb)
DOI: 10.6084/m9.figshare.c.3639053_d6.v1
title: Additional file 5: of Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network

description: Annotation of genes with confirmed expression patterns. This file is a subset of Additional file 4, and contains only genes for which patterned expression was detected. Classifications in this file were used to produce the charts in Fig.Â 3. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.c.3639059_d1.v1
title: Additional file 3: of Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection

description: GO enrichments. Gene set enrichments for housekeeping, up-regulated and down-regulated genes. Enriched GO categories among the up- and down-regulated antisense RNA in vivo are also shown.
DOI: 10.6084/m9.figshare.c.3639059_d3.v1
title: Additional file 1: of Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection

description: Primers. Primers used to validate expression pattern of RNA-seq data.
DOI: 10.6084/m9.figshare.c.3639059_d4.v1
title: Additional file 2: of Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection

description: Differential expression of Nagasaki genes. Differential expression of genes ex vivo versus plate culture (A), in vivo versus plate culture (B) and antisense RNA in vivo versus plate culture (C).
DOI: 10.6084/m9.figshare.c.3639059_d2.v1
title: Additional file 4: of Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection

description: Membrane genes. Membrane genes up-regulated in vivo, ex vivo or in both conditions. Differential expression is also shown.
DOI: 10.6084/m9.figshare.c.3639188_d7.v1
title: Additional file 9: of 
                     De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

description: Non-redundant putative transcripts identified using the University of Victoria consortium of genomics research on all salmon repeat database. (RAR 16480 kb)
DOI: 10.6084/m9.figshare.c.3639188_d8.v1
title: Additional file 6: of 
                     De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

description: Associated UniProt 2013_11 protein database annotation of all Sockey salmon head kidney unigene components. (RAR 14953 kb)
DOI: 10.6084/m9.figshare.c.3639191_d1.v1
title: Additional file 1: of The effect of foot orthoses with forefoot cushioning or metatarsal pad on forefoot peak plantar pressure in running

description: The dataset with the raw data of peak pressures for the total foot and the forefoot. (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.c.3639221_d2.v1
title: Additional file 1: of Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly

description: Supplementary Table 3.
DOI: 10.15468/dl.7p68zs
title: Occurrence Download

description: A dataset containing 672 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.52764 1.97919,-79.63203 0.41341,-75.24785 -1.04798,-73.36892 -3.24007,-70.6549 -5.22339,-68.25404 -4.17954,-69.29789 -0.00413,-66.27072 1.03972,-66.37511 5.73705,-68.5672 7.19844,-71.3856 10.01684,-70.02859 13.35717,-79.42326 9.80807,-78.58817 8.13791,-78.17063 4.58881,-79.52764 1.97919))",
 "TaxonKey is Melipona Illiger, 1806"
 ]
}

 The dataset includes 672 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038061-241126133413365/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.3639380_d1.v1
title: Additional file 2: Table S1. of Analysis of RNA expression of normal and cancer tissues reveals high correlation of COP9 gene expression with respiratory chain complex components

description: The let-7 expression profilesof the matched head and neck normal and tumor tissues. Correlation coefficients for individual let-7 isoforms relative to COP9 genes are shown. Asterisks: p &lt; 0.05. Table S2. To support the result of Table 3, 2 additional normal head and neck tissues were included to calculate correlation of expressions among the COP9 genes. Correlation coefficients of COP9 genes versus COPS5 (rCOPS5) were determined from randomly selected 44 tumor specimens from the entire pool of 511. The calculations were repeated for 10,000 times to obtain their mean and standard deviation (sd) values, which were used to compare the difference from rCOPS5 of normal tissues. Table S3. RNAseq data from young (30 specimens) and elderly patients (31 specimens) were used to calculate the correlation coefficients among the COP9 genes. Table S4. 14 normal oral cavity tissues were pooled based on the TCGA clinical data, and the correlation coefficients and their p values for COPS5 were calculated as described in the main article. Table S5. Data based on the 13 normal tongue tissues were pooled based on the clinical data in the TCGA database, and the correlation coefficients and their p values for COPS5 were calculated. Table S6. 11 normal tissues from smokers were pooled based on the clinical data in the TCGA database, and the correlation coefficients and their p values for COPS5 were calculated. Table S7. Nh: number of genes found within 1 Mbp of each COP9 gene; mean, sd, p and q values were determined as described in Materials and Methods. Table S8. ES for COP9 genes for all KEGG pathways. Table S9. ES for COP9 genes for the oxidative phosphorylation pathway. (XLS 80Â kb)
DOI: 10.6084/m9.figshare.c.3639380_d2.v1
title: Additional file 6: Table S13. of Analysis of RNA expression of normal and cancer tissues reveals high correlation of COP9 gene expression with respiratory chain complex components

description: GO and KEGG pathways over-represented in the normal and tumor lung tissues based on the COPS5 correlation coefficient table. (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.c.3639380_d5.v1
title: Additional file 3: Table S10. of Analysis of RNA expression of normal and cancer tissues reveals high correlation of COP9 gene expression with respiratory chain complex components

description: The COPS5 correlation coefficient table list includes 1000 highest |r| values relative to the expression of COPS5 in the normal and tumor tissues of head and neck. (XLSX 621Â kb)
DOI: 10.6084/m9.figshare.c.3639380_d4.v1
title: Additional file 7: Table S14. of Analysis of RNA expression of normal and cancer tissues reveals high correlation of COP9 gene expression with respiratory chain complex components

description: Genes under the chromosomal cis-effect in the HNSCC tissues (XLS 2117Â kb)
DOI: 10.6084/m9.figshare.c.3639380_d6.v1
title: Additional file 8: Table S15. of Analysis of RNA expression of normal and cancer tissues reveals high correlation of COP9 gene expression with respiratory chain complex components

description: KEGG pathway analysis for the TP53 gene (XLS 70Â kb)
DOI: 10.6084/m9.figshare.c.3639380_d7.v1
title: Additional file 5: Table S12. of Analysis of RNA expression of normal and cancer tissues reveals high correlation of COP9 gene expression with respiratory chain complex components

description: GO and KEGG pathways over-represented by COPS5 expression correlation in the two major anatomical sites in the head and neck (oral cavity and tongue). (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.c.3639380_d8.v1
title: Additional file 4: Table S11. of Analysis of RNA expression of normal and cancer tissues reveals high correlation of COP9 gene expression with respiratory chain complex components

description: GO and KEGG pathways that are over-represented in the normal and tumor oral tissues based on the COPS5 correlation coefficient table. (XLSX 147Â kb)
DOI: 10.6084/m9.figshare.c.3639389_d1.v1
title: MOESM1 of Convergent validity: agreement between accelerometry and the Global Physical Activity Questionnaire in college-age Saudi men

description: Additional file 1. Raw data of accelerometers and the Global Physical Activity Questionnaire in week 1 and 2, including sedentary, low, moderate and vigorous physical activity (nÂ =Â 62).
DOI: 10.6084/m9.figshare.c.3639392_d2.v1
title: Additional file 1: of Perceived barriers to success for resident physicians interested in immigrant and refugee health

description: Title of data: Raw Data Set. Description: Full raw data set via excel spreadsheet. (XLSX 93Â kb)
DOI: 10.6084/m9.figshare.c.3639398_d1.v1
title: MOESM3 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 3. k-s.r. Source code in R for estimating Kolmogorov-Smirnov inbreeding coefficients.
DOI: 10.6084/m9.figshare.c.3639398_d3.v1
title: MOESM5 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 5. Expon.r. Source code in R for estimating exponential inbreeding coefficients.