cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3603128_d5.v1
title: Additional file 8: of Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis

description: Summary of everything. Sheet 1: Stress Gene Survey. List of tissue-specific targets and their reciprocal best blast hit (accession ID) from the dataset presented by Reitzel et al [63]. Included fields: Tissue, unique transcript ID (NvecRef ID), reciprocal best blastx hit (Hit), stressor type (pathogen, wound, or chemical). Transcripts with reciprocal best blast hits involved in both pathogen and wound stress are indicated as: Pathogen.Wound. Sheet 2: Transcriptome Summary. Summary of all 17,313 transcripts used for differential expression and orthology analyses. Each entry contains the following: unique transcriptome ID (NvecRef ID), transcript length (in nucleotides), orthology group ID (GrID): N – Nematostella-specific, E – Edwarsiidae-specific, A – anthozoan-specific, C – cnidarian-specific, M – conserved/metazoan, number of tissues (out of three) in which the transcript is expressed, differential expression result (UP/mes is upregulated in the mesenteries relative to both other tissues), mean counts across all tissues (AllMean) and across replicates within a tissue (MesMean, NemMean, TenMean), log2 fold change for all pairwise tissue comparisons (negative values indicate upregulation in the second tissue), adjusted p-values/false discovery rates for all pairwise comparisons, and raw counts for each tissue replicate. Sheet 3: Alien Index Results. Fields: unique transcriptome ID (NvecRef ID), alien index (AI), % identity and coverage of the top blast hit, and whether the sequence was deemed present in the genome (http://genome.jgi.doe.gov/Nemve1/Nemve1.home.html). Sheet 4: Primers. Sequences for all primers used in qPCR and standard PCR analyses. Primer sequences for each transcript are presented 5’ → 3’. (XLSX 4037 kb)
DOI: 10.6084/m9.figshare.25336294
title: ePRS project: summary statistics and ancestry-specific allele frequency

description: Here we share the summary statistics and ancestry-specific allele frequencies for computing PRSs and expected PRSs (ePRSs) provided in the manuscript "The expected polygenic risk score (ePRS) framework: an equitable metric for quantifying polygenetic risk via modeling of ancestral makeup" (check out our preprint on medRxiv: https://medrxiv.org/cgi/content/short/2024.03.05.24303738v1)."All_sumstat.xlsx" contains all the summary statistics we used for the primary PRS-outcome association analyses."LDPred2_sumstat.xlsx" contains all the summary statistics we computed via LDPred2 method."TOPMed_ancestry_specific_AF_by_GAFA.xlsx" contains the ancestry-specific allele frequencies computed using data from individuals in TOPMed. The ancestry-specific allele frequency was computed based on the "ALT" allele using GAFA algorithm (more details of GAFA method can be found at: https://doi.org/10.1016/j.xhgg.2022.100096).The “Sumstat_and_ancestry_AF_AoU_analysis.zip” compressed file contains the summary statistics (download for PGS catalog) and ancestry-specific allele frequency (download for gnomAD) for computing 6 CVD-related PRSs and ePRSs in AoU analysis.<br>
DOI: 10.6084/m9.figshare.25336294.v1
title: ePRS project: summary statistics and ancestry-specific allele frequency

description: Here we share the summary statistics and ancestry-specific allele frequencies for computing PRSs and expected PRSs (ePRSs) provided in the manuscript "The expected polygenic risk score (ePRS) framework: an equitable metric for quantifying polygenetic risk via modeling of ancestral makeup" (check out our preprint on medRxiv: https://medrxiv.org/cgi/content/short/2024.03.05.24303738v1)."All_sumstat.xlsx" contains all the summary statistics we used for the primary PRS-outcome association analyses."LDPred2_sumstat.xlsx" contains all the summary statistics we computed via LDPred2 method."TOPMed_ancestry_specific_AF_by_GAFA.xlsx" contains the ancestry-specific allele frequencies computed using data from individuals in TOPMed. The ancestry-specific allele frequency was computed based on the "ALT" allele using GAFA algorithm (more details of GAFA method can be found at: https://doi.org/10.1016/j.xhgg.2022.100096).<br><br><br>
DOI: 10.15468/dl.7wwh8n
title: Occurrence Download

description: A dataset containing 46792 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Machine Observation, Human Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "StateProvince is one of (ARizona, Arizona, Arizona (State), Arizona (AZ))",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 46792 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037929-241126133413365/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.3603140_d3.v1
title: MOESM3 of Development of a high throughput drug screening assay to identify compounds that protect oligodendrocyte viability and differentiation under inflammatory conditions

description: Additional file 3: Table S2. NCC library cytokine protection screen data set.
DOI: 10.6084/m9.figshare.c.3603611_d2.v1
title: MOESM1 of A PCR assay detects a male-specific duplicated copy of Anti-MĂźllerian hormone (amh) in the lingcod (Ophiodon elongatus)

description: Additional file 1. Sampling information. Additional information on the collection of lingcod tissues used in the study.
DOI: 10.6084/m9.figshare.c.3603614_d2.v1
title: Additional file 2: of Uncovering obsessive-compulsive disorder risk genes in a pediatric cohort by high-resolution analysis of copy number variation

description: Table S1 (XLSX 63Â kb)
DOI: 10.5519/qd.tjfdnrii
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (43 records)
DOI: 10.6084/m9.figshare.c.3603614_d3.v1
title: Additional file 4: of Uncovering obsessive-compulsive disorder risk genes in a pediatric cohort by high-resolution analysis of copy number variation

description: Table S5 (XLSX 1313Â kb)
DOI: 10.6084/m9.figshare.c.3604085_d4.v1
title: Additional file 4: of Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution

description: Contains Table S1. The human Small-Scale and Whole-Genome duplicate pairs used in the study. (XLSX 705Â kb)
DOI: 10.6084/m9.figshare.c.3604028_d18.v1
title: Additional file 1: Table S1. of Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

description: Classification of fungal chitin synthase single mutants and comparison of their phenotype (1986–2016). In the first tab, phenotypes of mutants are summarized. In the second tab, phenotypes of mutants are detailed. In the third tab are the references of the single mutants publications. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3604106_d1.v1
title: Additional file 1: of EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms

description: Table of 42 echinoderm specimens used for RNA-seq data that are contained in http://echinodb.uncc.edu . The BJ number is an internal reference code. The voucher number represents where any residual tissues and metadata are stored. RAW indicates the number of raw reads produced by Illumina sequencing. Quality filter and adapter removal indicates the number of reads remaining following fastxtoolkit quality filter of Q score &gt; 20 and removal of adapter regions. Percent reads remaining indicates the fraction of raw reads retained after quality filtering and adapter removal. Percentage Reads removed indicates the fraction of reads removed by quality filtering and adapter removal from the raw reads. Number of Amino Acid Sequences Participating in Orthologous Clusters indicates number of contigs for each species that participated in orthoclusters. Note that contigs may be partially overlapping and redundant. NCBI BioProject Accession number indicates where the contigs have been submitted to NCBI (note the orthoclusters only exist on http://echinodb.uncc.edu ). (XLSX 33 kb)
DOI: 10.6084/m9.figshare.c.3604028_d20.v1
title: Additional file 12: File S1. of Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

description: Databank of all classified CHS in fasta format. (TXT 980 kb)
DOI: 10.6084/m9.figshare.c.3604550_d20.v1
title: Additional file 17: Table S17. of Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa

description: Changes of gene expression of the DEGs in the three samples. (XLSX 415 kb)
DOI: 10.6084/m9.figshare.c.3604607_d1.v1
title: Additional file 2: of Species and abundance of ectoparasitic flies (Diptera) in pied flycatcher nests in Fennoscandia

description: Genetic distances between individual sequences. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3604550_d25.v1
title: Additional file 14: Table S14. of Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa

description: Conserved miRNAs of P. tomentosa ath/aly: Arabidopsis; ptc: Populus trichocarp; osa: Oryza sativa; zma: Zea mays; gma: Glycine max;+: 2 mismatches; ++: 1 mismatches; +++: 0 mismatch; -: not exist. (XLS 51.0 kb)
DOI: 10.6084/m9.figshare.c.3604631_d1.v1
title: Additional file 13: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

description: GeneSCF v1.1 tool, documentation and instructions to run test dataset (case study 1 and 2) used in this study. (GZ 4447 kb)
DOI: 10.6084/m9.figshare.c.3605069_d1.v1
title: Additional file 3: Table S1. of deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

description: The mutational signature contribution to each TCGA tumor sample studied as determined by deconstructSigs and WTSI Mutational Signature Framework. Signatures used as input to deconstructSigs were limited to those extracted using the WTSI Mutational Signature Framework approach. (TXT 464 kb)
DOI: 10.15468/dl.pfq988
title: Occurrence Download

description: A dataset containing 659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "TaxonKey is Quercus canariensis Willd."
 ]
}

 The dataset includes 659 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037931-241126133413365/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.3605069_d2.v1
title: Additional file 7: Table S3. of deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

description: Mutations from TCGA ESCA cohort and their timing (early/late). (TXT 811 kb)
DOI: 10.15468/dl.955wue
title: Occurrence Download

description: A dataset containing 9181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((15 -18,16 -18,16 -19,15 -19,15 -18))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 9181 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037930-241126133413365/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.3605021_d10.v1
title: Additional file 12: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

description: Key differentially expressed genes discussed in the manuscript, based on their functional categories and expression profiles. Each sheet contains the genes in each cluster discussed. (XLSX 23094 kb)
DOI: 10.6084/m9.figshare.c.3605021_d11.v1
title: Additional file 9: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

description: Distribution of differentially expressed genes of each soil microorganism in 18 clusters, based on the expression profiles. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3605069_d6.v1
title: Additional file 6: Table S2. of deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

description: The mutational signature contribution to each TCGA tumor sample studied as determined by deconstructSigs and WTSI Mutational Signature Framework. The full published set of mutational signatures [4] was allowed to be used as input to deconstructSigs. Tumor types considered were limited to those where only unambiguous signatures could be extracted using the WTSI Mutational Signature Framework to allow for direct comparison with the input reference signature set. (TXT 359 kb)
DOI: 10.6084/m9.figshare.c.3605567_d4.v1
title: MOESM1 of Collapse of an iconic conifer: long-term changes in the demography of Widdringtonia cedarbergensis using repeat photography

description: Additional file 1: Table S1. Details of photographers for all 87 repeat photograph photo-pairs taken in the Cederberg Wilderness Area between 1931 and 2013.
DOI: 10.6084/m9.figshare.c.3605582_d1.v1
title: Additional file 2: of Charting the evolution of approaches employed by the Global Alliance for Vaccines and Immunizations (GAVI) to address inequities in access to immunization: a systematic qualitative review of GAVI policies, strategies and resource allocation mechanisms through an equity lens (1999â  2014)

description: Detailed literature results. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.c.3605591_d2.v1
title: Additional file 2: of Impact of tissue sampling on accuracy of Ki67 immunohistochemistry evaluation in breast cancer

description: Initial dataset of the study. (XLSX 2 mb)
DOI: 10.6084/m9.figshare.c.3606596_d1.v1
title: Additional file 1: of Bone marrow-derived mesenchymal stromal cells differ in their attachment to fibronectin-derived peptides from term placenta-derived mesenchymal stromal cells

description: Supplementary Table. Expression values (log2) of 593 significantly differentially expressed genes between bone marrow-derived mesenchymal stromal cells (Bm) and term placenta-derived mesenchymal stromal cells (P). Normalized expression values for all 25 samples are shown. Rightmost two columns show the combined log2 fold change between the two groups (logFC) and the absolute fold change (CFC). (XLSX 248 kb)
DOI: 10.5281/zenodo.14510248
title: Moving Moutons Dataset

description: This is Moving Moutons, the first publicly available dataset covering sheep herd movement observation from two perspectives. It contains GNSS coordinate measurements as well as video coverage from an elevated point of the field. This initial release of Moving Moutons covers a sample taken in the Swiss alps in August 2024. Its starting time is 08:10 on August 21. The CSV file contains a non-unique merged index column (can be ignored), longitude/latitude pairs in WGS84 coordinates, the timestamp of GNSS data acquisition (locally captured to avoid data gaps resulting from lossy transmissions), and a unique identifier for each animal in the herd.
DOI: 10.5281/zenodo.14510249
title: Moving Moutons Dataset

description: This is Moving Moutons, the first publicly available dataset covering sheep herd movement observation from two perspectives. It contains GNSS coordinate measurements as well as video coverage from an elevated point of the field. This initial release of Moving Moutons covers a sample taken in the Swiss alps in August 2024. Its starting time is 08:10 on August 21. The CSV file contains a non-unique merged index column (can be ignored), longitude/latitude pairs in WGS84 coordinates, the timestamp of GNSS data acquisition (locally captured to avoid data gaps resulting from lossy transmissions), and a unique identifier for each animal in the herd.
DOI: 10.6084/m9.figshare.c.3607067_d1.v1
title: Additional file 1: Table S1. of Comparison between two amplicon-based sequencing panels of different scales in the detection of somatic mutations associated with gastric cancer

description: Panel description and references. Table S2. Cutting areas of ESD-resected specimens (n=19) by laser capture microdissection and biopsies (n=2). Table S3. Assessment of tumor-derived DNA qualities. (XLS 43 kb)
DOI: 10.15468/dl.xqkmyd
title: Occurrence Download

description: A dataset containing 825 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.293 21.279,-100.178 21.279,-100.178 21.388,-100.293 21.388,-100.293 21.279))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 825 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037932-241126133413365/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.3607070_d1.v1
title: Additional file 5: of Genetic composition of captive panda population

description: Genetic composition and inbreeding coefficients of hypothetical offspring of the 1630 mating pairs free of pedigree and hidden inbreeding. (XLSX 463 kb)
DOI: 10.6084/m9.figshare.c.3607070_d2.v1
title: Additional file 3: of Genetic composition of captive panda population

description: Genetic composition of the new generation from the recommended mating pairs based on the MSI scores. (XLSX 3317 kb)
DOI: 10.6084/m9.figshare.c.3607088_d1.v1
title: MOESM3 of A retrospective analysis of eye conditions among children attending St. John Eye Hospital, Hebron, Palestine

description: Additional file 3: Table S3. â  Otherâ   conditions.
DOI: 10.6084/m9.figshare.c.3607097_d1.v1
title: Additional file 5: Table S5. of Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia

description: Fibroblast growth factor signalling genes with elevated Tajimaâ  s D, H W , and Ď . (XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3607097_d2.v1
title: Additional file 3: Table S4. of Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia

description: Gene models in outlier regions with H A /H S &gt;1. (XLS 59 kb)
DOI: 10.6084/m9.figshare.c.3607088_d2.v1
title: MOESM4 of A retrospective analysis of eye conditions among children attending St. John Eye Hospital, Hebron, Palestine

description: Additional file 4: Table S4. Conditions according to sex.
DOI: 10.6084/m9.figshare.c.3607097_d3.v1
title: Additional file 1: Table S2. of Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia

description: Gene models in genomic regions with outlier values of Tajimaâ  s D, H W , and/or Ď . (XLS 411 kb)
DOI: 10.6084/m9.figshare.c.3607070_d5.v1
title: Additional file 6: of Genetic composition of captive panda population

description: Genetic composition of the new generation from three plans of habitat-controlled breeding. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.c.3607541_d2.v1
title: Additional file 8: Table S2. of Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle

description: Excel file describing highly significant SNPs (genome-wise FDR ≤ 5 %, FDR ≤ 1% and genome-wise Bonferroni ≤ 5 %) resulting from GWAS using single SNP regression mixed linear model for calving to first service interval (CTFS) and days open (DO). (XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3607535_d3.v1
title: Additional file 2: of A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata

description: Presents in detail all clusters found in the final graph by our algorithm. The clusters are ordered by their numbers in column A; the first cluster is a giant one (shown partially). The first line of each cluster is marked with fixed numbers in columns C–D; it contains the number of vertices (words) of that cluster in column E. Each of the subsequent lines corresponds to a word and contains the following data in columns A–J: the cluster number (A), the number of species in the cluster (B), the vertex degree (C), the vertex density, i.e., the number of graph parts this vertex is connected to (D), the species name (E), the sequence name (F), start position of the word in the sequence (G), the word length (H), DNA strand indicator (I), and the word itself (J). A part of the word shown in capital letters corresponds to the intersection of all words merged at this vertex (a group); lowercase letters correspond to the union of those words. If the word overlaps with regions of a gene and its coding sequence (CDS) according to the genome annotation available in GenBank, this word corresponds to a protein. In such cases, the gene data including the protein description is shown in columns K–O; and CDS data, in columns P–R. If only the first condition is satisfied, the word belongs to a gene untranslated region such as an intron; in this case, only the data on the gene are shown. If a word is a fragment of a known non-protein-coding RNA according to Rfam database, columns S–AB contain the RNA name and other data. The clusters that correspond to untranslated regions or unknown HCEs are highlighted in gold or blue, respectively, in column A. (XLSX 10204 kb)
DOI: 10.6084/m9.figshare.c.3607538_d3.v1
title: Additional file 6: of A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

description: Relationship between miRNAs and experiment validated genes. (XLS 1416Â kb)
DOI: 10.6084/m9.figshare.c.3607541_d3.v1
title: Additional file 6: Table S7. of Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle

description: Common significant SNPs (genome-wise 1Â % FDR) identified among all production related traits (MILK, FAT, PROT, FATD, PROTD) using single SNP regression mixed linear model on imputed BovineHD (777Â k) genotypes in Holstein cattle. (XLS 43 kb)
DOI: 10.6084/m9.figshare.c.3607538_d4.v1
title: Additional file 7: of A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

description: Relationship between miRNAs, experiment validated genes and lncRNAs. (XLS 6019Â kb)
DOI: 10.6084/m9.figshare.c.3607541_d4.v1
title: Additional file 7: Table S8. of Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle

description: Common significant SNPs (genome-wise 1Â % FDR) identified among all fertility related traits (CTFS and DO) using single SNP regression mixed linear model on the imputed BovineHD (777Â k) genotypes in Holstein cattle. (XLS 34 kb)
DOI: 10.6084/m9.figshare.c.3607538_d5.v1
title: Additional file 5: of A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

description: Relationship between miRNAs and lncRNAs. (XLS 312Â kb)
DOI: 10.6084/m9.figshare.c.3607538_d6.v1
title: Additional file 1: of A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

description: Differentially expressed miRNAs. (XLS 24Â kb)
DOI: 10.6084/m9.figshare.c.3607538_d7.v1
title: Additional file 3: of A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

description: Differentially expressed known lncRNAs. (XLS 22Â kb)
DOI: 10.6084/m9.figshare.c.3607538_d8.v1
title: Additional file 8: of A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

description: GO enrichment analysis results of ceRNAs. (XLS 78Â kb)