cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3728767_d33
title: DRA002216

description: List of DRA (http://trace.ddbj.nig.ac.jp/dra/index_e.html) accession numbers
of the FANTOM5 samples, sequences and genomic coordinations.

Files are in tab-delimited format, which includes
* Library ID
* FFID
* BioSamples accession number
* DRA experiment accession number
* DRA run accession numbers
* DRA analysis accession number for genomic coordination (BAM file)
* DRA analysis accession number for CTSS (BED file)
* Experiment method (CAGE/RNA-Seq/sRNA-Seq)
DOI: 10.6084/m9.figshare.c.3728767_d32
title: DRA002747

description: List of DRA (http://trace.ddbj.nig.ac.jp/dra/index_e.html) accession numbers
of the FANTOM5 samples, sequences and genomic coordinations.

Files are in tab-delimited format, which includes
* Library ID
* FFID
* BioSamples accession number
* DRA experiment accession number
* DRA run accession numbers
* DRA analysis accession number for genomic coordination (BAM file)
* DRA analysis accession number for CTSS (BED file)
* Experiment method (CAGE/RNA-Seq/sRNA-Seq)
DOI: 10.6084/m9.figshare.c.3728767_d31.v1
title: DRA002711

description: List of DRA (http://trace.ddbj.nig.ac.jp/dra/index_e.html) accession numbers
of the FANTOM5 samples, sequences and genomic coordinations.

Files are in tab-delimited format, which includes
* Library ID
* FFID
* BioSamples accession number
* DRA experiment accession number
* DRA run accession numbers
* DRA analysis accession number for genomic coordination (BAM file)
* DRA analysis accession number for CTSS (BED file)
* Experiment method (CAGE/RNA-Seq/sRNA-Seq)
DOI: 10.6084/m9.figshare.c.3728767_d30.v1
title: DRA001028

description: List of DRA (http://trace.ddbj.nig.ac.jp/dra/index_e.html) accession numbers
of the FANTOM5 samples, sequences and genomic coordinations.

Files are in tab-delimited format, which includes
* Library ID
* FFID
* BioSamples accession number
* DRA experiment accession number
* DRA run accession numbers
* DRA analysis accession number for genomic coordination (BAM file)
* DRA analysis accession number for CTSS (BED file)
* Experiment method (CAGE/RNA-Seq/sRNA-Seq)
DOI: 10.6084/m9.figshare.c.3728767_d31
title: DRA002711

description: List of DRA (http://trace.ddbj.nig.ac.jp/dra/index_e.html) accession numbers
of the FANTOM5 samples, sequences and genomic coordinations.

Files are in tab-delimited format, which includes
* Library ID
* FFID
* BioSamples accession number
* DRA experiment accession number
* DRA run accession numbers
* DRA analysis accession number for genomic coordination (BAM file)
* DRA analysis accession number for CTSS (BED file)
* Experiment method (CAGE/RNA-Seq/sRNA-Seq)
DOI: 10.6084/m9.figshare.c.3728767_d30
title: DRA001028

description: List of DRA (http://trace.ddbj.nig.ac.jp/dra/index_e.html) accession numbers
of the FANTOM5 samples, sequences and genomic coordinations.

Files are in tab-delimited format, which includes
* Library ID
* FFID
* BioSamples accession number
* DRA experiment accession number
* DRA run accession numbers
* DRA analysis accession number for genomic coordination (BAM file)
* DRA analysis accession number for CTSS (BED file)
* Experiment method (CAGE/RNA-Seq/sRNA-Seq)
DOI: 10.15468/dl.d8qtsc
title: Occurrence Download

description: A dataset containing 1185 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.15524 10.37139,-74.902 10.18758,-74.72024 10.51026,-74.66714 10.91667,-74.84277 11.16787,-75.07151 10.99836,-75.30432 10.82477,-75.28186 10.66547,-75.26756 10.45512,-75.15524 10.37139))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 1185 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035499-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xupt43
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lophiomus laticeps (Ogilby, 1910)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035500-241126133413365/datasets/export for details.
DOI: 10.15468/dl.vyxgfn
title: Occurrence Download

description: A dataset containing 84084 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((99.2 26.8,100.2 26.8,100.2 28.3,99.2 28.3,99.2 26.8))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 84084 records from 201 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035498-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14496879
title: Molden files generated from cluster models of PARP-1/2 structures

description: Molden files generated from cluster models of PARP-1/2 in complex with inhibitors.
DOI: 10.5281/zenodo.14496880
title: Molden files generated from cluster models of PARP-1/2 structures

description: Molden files generated from cluster models of PARP-1/2 in complex with inhibitors.
DOI: 10.6084/m9.figshare.c.3729784_d4
title: Additional file 4: Table S4. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

description: The detailed features of genes completely or partial overlapped with differential CNVRs. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.c.3729784_d3
title: Additional file 3: Table S3. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

description: General statistics of 487 differential CNVRs between high and low group based on UMD3.1. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.c.3729784_d3.v1
title: Additional file 3: Table S3. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

description: General statistics of 487 differential CNVRs between high and low group based on UMD3.1. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.c.3729784_d2.v1
title: Additional file 2: Table S2. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

description: Primers information and confirmation results of the 11 chosen CNVRs by qPCR analysis. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3729784_d2
title: Additional file 2: Table S2. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

description: Primers information and confirmation results of the 11 chosen CNVRs by qPCR analysis. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3729784_d1.v1
title: Additional file 1: Table S1. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

description: Summary of identified CNVs and CNVRs in the 8 bullsâ   genomes. (XLSX 1044Â kb)
DOI: 10.6084/m9.figshare.c.3729784_d1
title: Additional file 1: Table S1. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

description: Summary of identified CNVs and CNVRs in the 8 bullsâ   genomes. (XLSX 1044Â kb)
DOI: 10.6084/m9.figshare.c.3729772_d1.v1
title: Additional file 1 of Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats

description: Table S3. Information on Repeats found in Pseudomonas aeruginosa strains. Table S4. Scaffolds of each of the 25 Pseudomonas aeruginosa strains. Table S5. Physical positions of repeats and breakpoints of rearrangements in Pseudomonas aeruginosa strains. Table S6. Scaffolds of each of the 31 Escherichia coli Strains. Table S7. Physical positions of repeats and breakpoints of rearrangements in Escherichia coli strains. Table S8. Information on repeats found in the Escherichia coli Strains. (XLSX 103 kb)
DOI: 10.6084/m9.figshare.c.3729772_d1
title: Additional file 1 of Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats

description: Table S3. Information on Repeats found in Pseudomonas aeruginosa strains. Table S4. Scaffolds of each of the 25 Pseudomonas aeruginosa strains. Table S5. Physical positions of repeats and breakpoints of rearrangements in Pseudomonas aeruginosa strains. Table S6. Scaffolds of each of the 31 Escherichia coli Strains. Table S7. Physical positions of repeats and breakpoints of rearrangements in Escherichia coli strains. Table S8. Information on repeats found in the Escherichia coli Strains. (XLSX 103 kb)
DOI: 10.6084/m9.figshare.c.3729697_d16.v1
title: Additional file 9 of Integrated analysis identifies microRNA-195 as a suppressor of Hippo-YAP pathway in colorectal cancer

description: Table S7. 11 underexpressed miRNAs validation results in TCGA-COAD dataset. (XLS 96Â kb)
DOI: 10.15468/dl.58xdeu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lophius setigerus Vahl, 1797",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035502-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3729697_d12
title: Additional file 5: of Integrated analysis identifies microRNA-195 as a suppressor of Hippo-YAP pathway in colorectal cancer

description: Table S3. Datasets used in final quantitative synthesis and integrated analysis. Contributor, assay type, platform, source accession, and PMID were listed alongside sample size (normal/tumor). (XLS 27Â kb)
DOI: 10.6084/m9.figshare.c.3729697_d11.v1
title: Additional file 4: of Integrated analysis identifies microRNA-195 as a suppressor of Hippo-YAP pathway in colorectal cancer

description: Table S2. The 23 full data sets which were potentially relevant studies assessed for eligibility. Contributor, assay type, platform, source accession, and PMID were listed alongside sample size (normal/tumor). (XLS 34Â kb)
DOI: 10.6084/m9.figshare.c.3729697_d11
title: Additional file 4: of Integrated analysis identifies microRNA-195 as a suppressor of Hippo-YAP pathway in colorectal cancer

description: Table S2. The 23 full data sets which were potentially relevant studies assessed for eligibility. Contributor, assay type, platform, source accession, and PMID were listed alongside sample size (normal/tumor). (XLS 34Â kb)
DOI: 10.15468/dl.fqh3sn
title: Occurrence Download

description: A dataset containing 23169 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "Geometry POLYGON ((144.5845 -29.60411, 145.4828 -29.60411, 145.4828 -28.70579, 144.5845 -28.70579, 144.5845 -29.60411))",
 "Year is less than 2025"
 ]
}

 The dataset includes 23169 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035501-241126133413365/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.3729754_d1
title: Additional file 1: Table S1. of Excessive activation of the TLR9/TGF-Î˛1/PDGF-B pathway in the peripheral blood of patients with systemic lupus erythematosus

description: Clinical data of the study subjects. (XLS 23 kb)
DOI: 10.6084/m9.figshare.c.3729754_d1.v1
title: Additional file 1: Table S1. of Excessive activation of the TLR9/TGF-Î˛1/PDGF-B pathway in the peripheral blood of patients with systemic lupus erythematosus

description: Clinical data of the study subjects. (XLS 23 kb)
DOI: 10.6084/m9.figshare.c.3729730_d5.v1
title: Additional file 4: of Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome

description: P-values and log2 fold-change resulting from testing miRNA differential expression between one miRNA cluster versus all other clusters using Wilcoxon rank-sum tests. P-values are corrected for multiple testing using Benjamini-Hochberg false discovery rate correction. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.c.3729730_d5
title: Additional file 4: of Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome

description: P-values and log2 fold-change resulting from testing miRNA differential expression between one miRNA cluster versus all other clusters using Wilcoxon rank-sum tests. P-values are corrected for multiple testing using Benjamini-Hochberg false discovery rate correction. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.c.3729697_d8
title: Additional file 1: of Integrated analysis identifies microRNA-195 as a suppressor of Hippo-YAP pathway in colorectal cancer

description: Table S1. The full-detailed search strategy and searching terms through PubMed, GEO, and Array Express databases. (XLS 26Â kb)
DOI: 10.6084/m9.figshare.c.3729697_d8.v1
title: Additional file 1: of Integrated analysis identifies microRNA-195 as a suppressor of Hippo-YAP pathway in colorectal cancer

description: Table S1. The full-detailed search strategy and searching terms through PubMed, GEO, and Array Express databases. (XLS 26Â kb)
DOI: 10.5281/zenodo.11124066
title: Data from: Accelerating adaptive trait divergence of annual plants in response to urban habitat diversity in a megacity

description: Data from the common garden experiment, field environmental factors, and data for Qst-Fst comparisons.
DOI: 10.5281/zenodo.14410947
title: Data from: Adaptive trait divergence of annual plants in response to urban habitat diversity in a megacity

description: Data from the common garden experiment, field environmental factors, and data for Qst-Fst comparisons.
DOI: 10.6084/m9.figshare.c.3728767_d25
title: expression table of the mouse CAGE peaks

description: CAGE peak based expression table (RLE normalized) for mouse samples
DOI: 10.6084/m9.figshare.c.3728767_d24
title: sample information of the human samples

description: Sample information (SDRF file) for human, including their details and details of their RNA extractions
DOI: 10.6084/m9.figshare.c.3728767_d24.v1
title: sample information of the human samples

description: Sample information (SDRF file) for human, including their details and details of their RNA extractions
DOI: 10.6084/m9.figshare.c.3728767_d23.v1
title: expression table of the human CAGE peaks

description: CAGE peak based expression table (RLE normalized) for human samples
DOI: 10.6084/m9.figshare.c.3728767_d22.v1
title: genomic coordinates of the mouse CAGE peaks

description: bed file of the mouse CAGE peaks
DOI: 10.6084/m9.figshare.c.3728767_d23
title: expression table of the human CAGE peaks

description: CAGE peak based expression table (RLE normalized) for human samples
DOI: 10.15468/dl.x4csbu
title: Occurrence Download

description: A dataset containing 260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphioctopus fangsiao (d'Orbigny, 1839)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 260 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035504-241126133413365/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.3728767_d22
title: genomic coordinates of the mouse CAGE peaks

description: bed file of the mouse CAGE peaks
DOI: 10.6084/m9.figshare.c.3728767_d21.v1
title: annotations of the mouse CAGE peaks

description: CAGE peak based table with annotated peaks for mouse samples
DOI: 10.6084/m9.figshare.c.3728767_d21
title: annotations of the mouse CAGE peaks

description: CAGE peak based table with annotated peaks for mouse samples
DOI: 10.6084/m9.figshare.c.3728767_d20
title: annotations of the human CAGE peaks

description: CAGE peak based table with annotated peaks for human samples
DOI: 10.6084/m9.figshare.c.3728767_d20.v1
title: annotations of the human CAGE peaks

description: CAGE peak based table with annotated peaks for human samples
DOI: 10.6084/m9.figshare.c.3728767_d19.v1
title: assay information of the unclassified samples for HeliScopeCAGE

description: a tab delimited flat file (SDRF file) describing the experimental details for unclassified samples for the standard protocol of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d19
title: assay information of the unclassified samples for HeliScopeCAGE

description: a tab delimited flat file (SDRF file) describing the experimental details for unclassified samples for the standard protocol of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d18
title: genomic coordinates of the human CAGE peaks

description: bed file of the human CAGE peaks
DOI: 10.6084/m9.figshare.c.3728767_d18.v1
title: genomic coordinates of the human CAGE peaks

description: bed file of the human CAGE peaks
DOI: 10.6084/m9.figshare.c.3728767_d17.v1
title: assay information of the mouse tissue samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse tissue samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d17
title: assay information of the mouse tissue samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse tissue samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d16
title: assay information of the mouse timecourse samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse timecousrse samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d16.v1
title: assay information of the mouse timecourse samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse timecousrse samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d15.v1
title: assay information of the mouse qualitycontrol samples for HeliScopeCAGE

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse quality control samples for the standard protocol of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d15
title: assay information of the mouse qualitycontrol samples for HeliScopeCAGE

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse quality control samples for the standard protocol of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d14.v1
title: assay information of the mouse qualitycontrol samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse quality control samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d14
title: assay information of the mouse qualitycontrol samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse quality control samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d9
title: assay information of the mouse qualitycontrol samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse quality control samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.6084/m9.figshare.c.3728767_d9.v1
title: assay information of the mouse primary cell samples for HeliScopeCAGE (low quantity ver.)

description: a tab delimited flat file (SDRF file) describing the experimental details for mouse primary cell samples for the low quantity version of the HeliScopeCAGE protocol
DOI: 10.15468/dl.ad9h5k
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ferula ammoniacum (D.Don) Spalik, M.Panahi, Piwczyñski & Puchalka"
 ]
}

 The dataset includes 16 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035508-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z48432
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Octopus fangsiao d'Orbigny",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035509-241126133413365/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.3726193_d4
title: Additional file 4 of Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite

description: Datasets for the comparison of different miRNA-disease association prediction models. This file contains the three datasets that used in three state-of-the-art methods such as RLSMDA, Xuâ  s method and Jiangâ  s method.This file can also be downloaded from: https://drive.google.com/open?id=0B6lH3mKdA9CSTkg2OVBPS0ZfVnM . (XLS 157 kb)
DOI: 10.6084/m9.figshare.c.3726181_d5.v1
title: Additional file 5: Table S5. of Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome

description: Tandem duplicated genes in S. indicum. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.c.3726181_d5
title: Additional file 5: Table S5. of Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome

description: Tandem duplicated genes in S. indicum. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.c.3726193_d3
title: Additional file 3 of Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite

description: Supplementary codes and data. The matlab codes of our methods and the input datasets. The data can also be downloaded from the following website: https://drive.google.com/open?id=0B6lH3mKdA9CSWDJHaWpnSUlPbGc . (ZIP 3080 kb)
DOI: 10.6084/m9.figshare.c.3726193_d3.v1
title: Additional file 3 of Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite

description: Supplementary codes and data. The matlab codes of our methods and the input datasets. The data can also be downloaded from the following website: https://drive.google.com/open?id=0B6lH3mKdA9CSWDJHaWpnSUlPbGc . (ZIP 3080 kb)
DOI: 10.6084/m9.figshare.c.3726181_d4
title: Additional file 4: Table S4. of Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome

description: Functional divergence of different classes of duplicated gene pairs between the two subgenomes in S. indicum. (XLSX 172 kb)
DOI: 10.6084/m9.figshare.c.3726181_d4.v1
title: Additional file 4: Table S4. of Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome

description: Functional divergence of different classes of duplicated gene pairs between the two subgenomes in S. indicum. (XLSX 172 kb)