cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22336033
title: Enhancer-Promoter Linkage Atlas for the Mouse Adipose tissue generated with Enhlink. Insights into Type II Diabetes Mechanisms and Covariate-Specific Regulation

description: These atlases were generated using single-nucleus ATAC-seq datasets from mouse Islet and Adipose tissues. The aim of the single-cell study on the Islet and Adipose tissues was to understand the genetic-specific mechanisms involved in the development of type II diabetes. The researchers created cell-type specific enhancer-promoter atlases for both tissues, identifying which linkages were specific to the strain, diet, and sex and which intersected with the pcHI-C datasets generated from the same tissues.<br><b>File descriptions</b>Each BEDPE file contains genomic links using the 6 first columns to define the enhancer (three first columns) and the promoter (the following three columns). Also, each file refers to a specific cell type written in the file name. The extension pchic refers to the links intersecting the ilset pcHI-C data. The extension unique refers to link unique within a cell type and not found in any of the other cell types.the extension 2ndOrder refers to covariate-specific links with the covariate ID described in one of the columns. Finally, the batch.tsv file describes the covariates associated with each promoter activity.<b>Methods</b>We independently processed each cell type of the tissue, considering library ID, sex, diet, and strain as covariates. We applied a p-value cutoff of 0.01 with the secondOrder option and used only 66% of the features, a maximum of 4 features, a depth of 2, and a downsampling size of 15,000 cells to obtain covariate-specific linkages for each tree. We generated a binary cell x promoter sparse matrix by setting 1 for a given gene g and cell c if at least one read from c fell into the promoter regions of g, and used the ATACMatUtils command with the -use_symbol option from the ATACdemultiplex package to create the matrix from the BED file containing the reads and barcode IDs. Finally, we used the enhtools software with the -intersect3 option to intersect the obtained linkage of each cell type with the pcHI-C links of either the Adipose or the Islet tissues.<br><b>Software</b>https://gitlab.com/Grouumf/enhlinktools<b>Citation</b>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03374-9<br>
DOI: 10.6084/m9.figshare.22336033.v3
title: Enhancer-Promoter Linkage Atlas for the Mouse Adipose tissue generated with Enhlink. Insights into Type II Diabetes Mechanisms and Covariate-Specific Regulation

description: These atlases were generated using single-nucleus ATAC-seq datasets from mouse Islet and Adipose tissues. The aim of the single-cell study on the Islet and Adipose tissues was to understand the genetic-specific mechanisms involved in the development of type II diabetes. The researchers created cell-type specific enhancer-promoter atlases for both tissues, identifying which linkages were specific to the strain, diet, and sex and which intersected with the pcHI-C datasets generated from the same tissues.<br><b>File descriptions</b>Each BEDPE file contains genomic links using the 6 first columns to define the enhancer (three first columns) and the promoter (the following three columns). Also, each file refers to a specific cell type written in the file name. The extension pchic refers to the links intersecting the ilset pcHI-C data. The extension unique refers to link unique within a cell type and not found in any of the other cell types.the extension 2ndOrder refers to covariate-specific links with the covariate ID described in one of the columns. Finally, the batch.tsv file describes the covariates associated with each promoter activity.<b>Methods</b>We independently processed each cell type of the tissue, considering library ID, sex, diet, and strain as covariates. We applied a p-value cutoff of 0.01 with the secondOrder option and used only 66% of the features, a maximum of 4 features, a depth of 2, and a downsampling size of 15,000 cells to obtain covariate-specific linkages for each tree. We generated a binary cell x promoter sparse matrix by setting 1 for a given gene g and cell c if at least one read from c fell into the promoter regions of g, and used the ATACMatUtils command with the -use_symbol option from the ATACdemultiplex package to create the matrix from the BED file containing the reads and barcode IDs. Finally, we used the enhtools software with the -intersect3 option to intersect the obtained linkage of each cell type with the pcHI-C links of either the Adipose or the Islet tissues.<br><b>Software</b>https://gitlab.com/Grouumf/enhlinktools<b>Citation</b>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03374-9<br>
DOI: 10.6084/m9.figshare.22336033.v2
title: Enhancer-Promoter Linkage Atlas for the Mouse Adipose tissue generated with Enhlink. Insights into Type II Diabetes Mechanisms and Covariate-Specific Regulation

description: These atlases were generated using single-nucleus ATAC-seq datasets from mouse Islet and Adipose tissues. The aim of the single-cell study on the Islet and Adipose tissues was to understand the genetic-specific mechanisms involved in the development of type II diabetes. The researchers created cell-type specific enhancer-promoter atlases for both tissues, identifying which linkages were specific to the strain, diet, and sex and which intersected with the pcHI-C datasets generated from the same tissues.
<br>
<strong>File descriptions</strong>
Each BEDPE file contains genomic links using the 6 first columns to define the enhancer (three first columns) and the promoter (the following three columns). Also, each file refers to a specific cell type written in the file name. The  extension pchic refers to the links intersecting the ilset pcHI-C data. The extension unique refers to link unique within a cell type and not found in any of the other cell types.the extension 2ndOrder refers to covariate-specific links with the covariate ID described in one of the columns.  Finally, the batch.tsv file describes the covariates associated with each promoter activity.
<strong>Methods</strong>
We independently processed each cell type of the tissue, considering library ID, sex, diet, and strain as covariates. We applied a p-value cutoff of 0.01 with the secondOrder option and used only 66% of the features, a maximum of 4 features, a depth of 2, and a downsampling size of 15,000 cells to obtain covariate-specific linkages for each tree. We generated a binary cell x promoter sparse matrix by setting 1 for a given gene g and cell c if at least one read from c fell into the promoter regions of g, and used the ATACMatUtils command with the -use_symbol option from the ATACdemultiplex package to create the matrix from the BED file containing the reads and barcode IDs. Finally, we used the enhtools software with the -intersect3 option to intersect the obtained linkage of each cell type with the pcHI-C links of either the Adipose or the Islet tissues.
<br>
https://gitlab.com/Grouumf/enhlinktools
DOI: 10.6084/m9.figshare.22335919
title: Enhancer-Promoter Linkage Atlas for the Mouse Islet tissue generated with Enhlink. Insights into Type II Diabetes Mechanisms and Covariate-Specific Regulation

description: These atlases were generated using single-nucleus ATAC-seq datasets from mouse Islet and Adipose tissues. The aim of the single-cell study on the Islet and Adipose tissues was to understand the genetic-specific mechanisms involved in the development of type II diabetes. The researchers created cell-type specific enhancer-promoter atlases for both tissues, identifying which linkages were specific to the strain, diet, and sex and which intersected with the pcHI-C datasets generated from the same tissues.<b>File descriptions</b>Each BEDPE file contains genomic links using the 6 first columns to define the enhancer (three first columns) and the promoter (the following three columns). Also, each file refers to a specific cell type written in the file name. The extension pchic refers to the links intersecting the ilset pcHI-C data. The extension unique refers to link unique within a cell type and not found in any of the other cell types.the extension 2ndOrder refers to covariate-specific links with the covariate ID described in one of the columns. Finally, the batch.tsv file describes the covariates associated with each promoter activity.<b>Methods</b>We independently processed each cell type of the tissue, considering library ID, sex, diet, and strain as covariates. We applied a p-value cutoff of 0.01 with the secondOrder option and used only 66% of the features, a maximum of 4 features, a depth of 2, and a downsampling size of 15,000 cells to obtain covariate-specific linkages for each tree. We generated a binary cell x promoter sparse matrix by setting 1 for a given gene g and cell c if at least one read from c fell into the promoter regions of g, and used the ATACMatUtils command with the -use_symbol option from the ATACdemultiplex package to create the matrix from the BED file containing the reads and barcode IDs. Finally, we used the enhtools software with the -intersect3 option to intersect the obtained linkage of each cell type with the pcHI-C links of either the Adipose or the Islet tissues.<b>Software</b>https://gitlab.com/Grouumf/enhlinktools<b>Citation</b>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03374-9
DOI: 10.6084/m9.figshare.22335919.v2
title: Enhancer-Promoter Linkage Atlas for the Mouse Islet tissue generated with Enhlink. Insights into Type II Diabetes Mechanisms and Covariate-Specific Regulation

description: These atlases were generated using single-nucleus ATAC-seq datasets from mouse Islet and Adipose tissues. The aim of the single-cell study on the Islet and Adipose tissues was to understand the genetic-specific mechanisms involved in the development of type II diabetes. The researchers created cell-type specific enhancer-promoter atlases for both tissues, identifying which linkages were specific to the strain, diet, and sex and which intersected with the pcHI-C datasets generated from the same tissues.
File descriptions
Each BEDPE file contains genomic links using the 6 first columns to define the enhancer (three first columns) and the promoter (the following three columns). Also, each file refers to a specific cell type written in the file name. The  extension pchic refers to the links intersecting the ilset pcHI-C data. The extension unique refers to link unique within a cell type and not found in any of the other cell types.the extension 2ndOrder refers to covariate-specific links with the covariate ID described in one of the columns.  Finally, the batch.tsv file describes the covariates associated with each promoter activity.
Methods
We independently processed each cell type of the tissue, considering library ID, sex, diet, and strain as covariates. We applied a p-value cutoff of 0.01 with the secondOrder option and used only 66% of the features, a maximum of 4 features, a depth of 2, and a downsampling size of 15,000 cells to obtain covariate-specific linkages for each tree. We generated a binary cell x promoter sparse matrix by setting 1 for a given gene g and cell c if at least one read from c fell into the promoter regions of g, and used the ATACMatUtils command with the -use_symbol option from the ATACdemultiplex package to create the matrix from the BED file containing the reads and barcode IDs. Finally, we used the enhtools software with the -intersect3 option to intersect the obtained linkage of each cell type with the pcHI-C links of either the Adipose or the Islet tissues.
<br>
https://gitlab.com/Grouumf/enhlinktools
<br>
DOI: 10.6084/m9.figshare.22335919.v3
title: Enhancer-Promoter Linkage Atlas for the Mouse Islet tissue generated with Enhlink. Insights into Type II Diabetes Mechanisms and Covariate-Specific Regulation

description: These atlases were generated using single-nucleus ATAC-seq datasets from mouse Islet and Adipose tissues. The aim of the single-cell study on the Islet and Adipose tissues was to understand the genetic-specific mechanisms involved in the development of type II diabetes. The researchers created cell-type specific enhancer-promoter atlases for both tissues, identifying which linkages were specific to the strain, diet, and sex and which intersected with the pcHI-C datasets generated from the same tissues.<b>File descriptions</b>Each BEDPE file contains genomic links using the 6 first columns to define the enhancer (three first columns) and the promoter (the following three columns). Also, each file refers to a specific cell type written in the file name. The extension pchic refers to the links intersecting the ilset pcHI-C data. The extension unique refers to link unique within a cell type and not found in any of the other cell types.the extension 2ndOrder refers to covariate-specific links with the covariate ID described in one of the columns. Finally, the batch.tsv file describes the covariates associated with each promoter activity.<b>Methods</b>We independently processed each cell type of the tissue, considering library ID, sex, diet, and strain as covariates. We applied a p-value cutoff of 0.01 with the secondOrder option and used only 66% of the features, a maximum of 4 features, a depth of 2, and a downsampling size of 15,000 cells to obtain covariate-specific linkages for each tree. We generated a binary cell x promoter sparse matrix by setting 1 for a given gene g and cell c if at least one read from c fell into the promoter regions of g, and used the ATACMatUtils command with the -use_symbol option from the ATACdemultiplex package to create the matrix from the BED file containing the reads and barcode IDs. Finally, we used the enhtools software with the -intersect3 option to intersect the obtained linkage of each cell type with the pcHI-C links of either the Adipose or the Islet tissues.<b>Software</b>https://gitlab.com/Grouumf/enhlinktools<b>Citation</b>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03374-9
DOI: 10.15468/dl.mtbpgx
title: Occurrence Download

description: A dataset containing 363159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "StateProvince is MInnesota",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 363159 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115114-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.puzhh6
title: Occurrence Download

description: A dataset containing 4049 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Dipodomys merriami ambiguus Merriam, 1890"
 ]
}

 The dataset includes 4049 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115127-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8vvmz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Liasis dunni Stull, 1932)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050327-230224095556074/datasets/export for details.
DOI: 10.25549/pcra-c14-62699
title: Redemption tidings, vol. 43, nos. 1-52, 6 Jan. - 28 Dec. 1967

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle for vol. 43, nos. 1-39 (6 Jan. - 29 Sept. 1967).
DOI: 10.15468/dl.mh9w3g
title: Occurrence Download

description: A dataset containing 1261906 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Nahant Collection"
 ]
}

 The dataset includes 1261906 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078763-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-62661
title: Redemption tidings, vol. 43, nos. 1-52, 6 Jan. - 28 Dec. 1967

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle for vol. 43, nos. 1-39 (6 Jan. - 29 Sept. 1967).
DOI: 10.15468/dl.vfxfwd
title: Occurrence Download

description: A dataset containing 1122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-151.05572 15.78680,-44.94428 15.78680,-44.94428 58.21320,-151.05572 58.21320,-151.05572 15.78680))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aeoloplides turnbulli (Thomas, 1872)"
 ]
}

 The dataset includes 1122 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050313-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7g5vj
title: Occurrence Download

description: A dataset containing 15833 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Andropogon gerardii Vitman"
 ]
}

 The dataset includes 15833 records from 225 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0401464-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.63cvrt
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "Geometry POLYGON ((-69.88223 12.41111, -69.94695 12.43667, -70.05612 12.53444, -70.05945 12.53806, -70.06029 12.54417, -70.06334 12.62167, -70.06306 12.62861, -70.05890 12.63111, -70.05334 12.62972, -70.03528 12.61972, -70.03111 12.61694, -69.93224 12.52806, -69.89696 12.48083, -69.89140 12.47222, -69.88556 12.45778, -69.87390 12.42194, -69.87334 12.41583, -69.87611 12.41166, -69.88223 12.41111))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 173 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037985-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-62797
title: Redemption tidings, vol. 43, nos. 1-52, 6 Jan. - 28 Dec. 1967

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle for vol. 43, nos. 1-39 (6 Jan. - 29 Sept. 1967).
DOI: 10.15468/dl.s3j8zb
title: Occurrence Download

description: A dataset containing 1526 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schizopora paradoxa (Schrad.) Donk",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is Switzerland",
 "Country is Switzerland"
 ]
 }
 ]
}

 The dataset includes 1526 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0401479-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e7ycuf
title: Occurrence Download

description: A dataset containing 30368 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Bituminaria bituminosa (L.) C.H.Stirt."
 ]
}

 The dataset includes 30368 records from 206 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050350-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-61720
title: Redemption tidings, vol. 42, nos. 1-52, 1 Jan. - 23 Dec. 1966

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.25549/pcra-c14-61562
title: Redemption tidings, vol. 42, nos. 1-52, 1 Jan. - 23 Dec. 1966

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.fr7rpu
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhadinella godmani (Günther, 1865))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 123 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050339-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wqfbwx
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fomitiporia robusta (P.Karst.) Fiasson & Niemelä",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is Switzerland",
 "Country is Switzerland"
 ]
 }
 ]
}

 The dataset includes 177 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0401467-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-61598
title: Redemption tidings, vol. 42, nos. 1-52, 1 Jan. - 23 Dec. 1966

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.4v3hwt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caliciopsis pseudotsugae Fitzp.",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is Switzerland",
 "Country is Switzerland"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0401482-210914110416597/datasets/export for details.
DOI: 10.15468/dl.qvrb6k
title: Occurrence Download

description: A dataset containing 892 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Brickellia eupatorioides var. corymbulosa (Torr. & A.Gray) Shinners"
 ]
}

 The dataset includes 892 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052162-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-68683
title: Redemption tidings, vol. 49, nos. 1-52, 4 Jan. - 27 Dec. 1973

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.fe75da
title: Occurrence Download

description: A dataset containing 463 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Untangling the waterfall damsels: a review of the Mesoamerican genus Paraphlebia Selys in Hagen, 1861 (Odonata: Thaumatoneuridae) with descriptions of 11 new species"
 ]
}

 The dataset includes 463 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050364-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.