cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.kej2zu
title: Occurrence Download

description: A dataset containing 1016 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Orchis anatolica Boiss.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1016 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001222-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69js9m
title: Occurrence Download

description: A dataset containing 7065 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Madagascar",
 "OccurrenceStatus is Present",
 "TaxonKey is Arecaceae"
 ]
}

 The dataset includes 7065 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0146108-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkarcc
title: Occurrence Download

description: A dataset containing 2315 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lomelosia graminifolia (L.) Greuter & Burdet",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2315 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001219-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9t4cjc
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lomelosia sphaciotica (Roem. & Schult.) Greuter & Burdet",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001233-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uycnj8
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blepharis hildebrandtii Lindau"
 ]
}

 The dataset includes 30 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0056804-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ncnwr
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Eriobotrya japonica (Thunb.) Lindl."
 ]
}

 The dataset includes 273 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081647-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.begefs
title: Occurrence Download

description: A dataset containing 772 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Freshwater Lamprey Survey Data"
 ]
}

 The dataset includes 772 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004855-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t3d9zh
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantago cornuti Gouan",
 "Year 1970-2020"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001208-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.thmhfg
title: Occurrence Download

description: A dataset listing the 18 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Freshwater Lamprey Survey Data"
 ]
}

 The dataset's 18 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004850-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnfwbb
title: Occurrence Download

description: A dataset containing 772 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Freshwater Lamprey Survey Data"
 ]
}

 The dataset includes 772 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004860-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8h6fdj
title: Occurrence Download

description: A dataset containing 1561 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Gunma Museum of Natural History, Mammal Specimen"
 ]
}

 The dataset includes 1561 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004871-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vbfnka
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corylus fargesii (Franch.) C.K.Schneid."
 ]
}

 The dataset includes 113 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013366-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjhvt0
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Xylopia ligustrifolia Humb. & Bonpl. ex Dunal",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 72 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045411-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xdynt7
title: Occurrence Download

description: A dataset containing 553 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "Country is Spain",
 "DatasetKey is one of (CSIC-Real Jardín Botánico-Colección de Plantas Vasculares (MA), Pl@ntNet observations, iNaturalist Research-grade Observations, Institut Botanic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), BC-Plantae, CSIC-Real Jardín Botánico-Anthos. Sistema de Información de las Plantas de España, CeDoc de Biodiversitat Vegetal: BCN-Cormophyta, Sistema de Información de la vegetación Ibérica y Macaronésica, FloraCAT: Banco de datos de los cormófitos de Cataluña, Colección de plantas vasculares del herbario de la Universitat de València (VAL), Herbarium of Vascular Plants Collection of the University of Extremadura (Spain))",
 "Geometry POLYGON((0.61101 42.86835,0.326 41.06732,0.64987 40.50823,1.12921 40.79327,3.33154 41.84405,3.38336 42.43004,3.02063 42.58285,2.52834 42.47784,0.61101 42.86835))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio lividus L."
 ]
}

 The dataset includes 553 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081653-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uvkdst
title: Occurrence Download

description: A dataset containing 141976 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamium amplexicaule L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 141976 records from 1021 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004858-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awhnww
title: Occurrence Download

description: A dataset containing 8985 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Phenology and biological traits of migrating river lamprey (Lampetra fluviatilis) sampled by trapping in the Bresle river (France)."
 ]
}

 The dataset includes 8985 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004853-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sz5vqg
title: Occurrence Download

description: A dataset containing 1141 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Luehea seemannii Planch. & Triana"
 ]
}

 The dataset includes 1141 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0146109-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5vv38y
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lonas annua (L.) Vines & Druce",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 72 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001240-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qjp2af
title: Occurrence Download

description: A dataset containing 772 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Freshwater Lamprey Survey Data"
 ]
}

 The dataset includes 772 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004868-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.webcce
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Blatticola blattae (Graeffe, 1860))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044600-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txkusc
title: Occurrence Download

description: A dataset containing 323 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lomelosia cretica (L.) Greuter & Burdet",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 323 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001216-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10563104
title: Gene Enhancer Predictions in C2C12 (Mouse Myoblast)

description: This file contains the complete enhancer prediction output of the analysis done in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

using the Activity by Contact Model following the pipeline described here: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

To be used in this analysis, a genomewide Hi-C interaction matrix was generated with Juicer  v1.6, expression counts for each gene were generated with STAR v2.7.10b and Rsubread v2.8.2, and the sequence alignment maps of ATAC-seq and H3K27ac ChIP-seq were generated with NextGenMap v0.5.5, all using raw sequencing reads downloaded from SRA: Hi-C (SRR16220088), RNA-seq (SRR074113 and SRR074114), ATAC-seq (SRR2999996) and H3K27ac ChIP-seq (SRR358589, SRR358590, and SRR358591).

The chromosome coordinates are of the GRCm38 - mm10 assembly, and the gene IDs are from ENSEMBL annotation.

Please use the Version 3, and for more information please refer to our publication that used these enhancer predictions.
DOI: 10.5281/zenodo.10563105
title: Please Use The Version 3

description: This file contains the complete enhancer prediction output of the analysis done using the Activity by Contact Model following the pipeline described here: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

To be used in this analysis, a genomewide Hi-C interaction matrix was generated with Juicer  v1.6, expression counts for each gene were generated with STAR v2.7.10b and Rsubread v2.8.2, and the sequence alignment maps of ATAC-seq and H3K27ac ChIP-seq were generated with NextGenMap v0.5.5, all using raw sequencing reads downloaded from SRA: Hi-C (SRR16220088), RNA-seq (SRR074113 and SRR074114), ATAC-seq (SRR2999996) and H3K27ac ChIP-seq (SRR358603 and SRR358604).

The chromosome coordinates are of the GRCm38 - mm10 assembly, and the gene IDs are from ENSEMBL annotation.

For more information please refer to our publication that used these enhancer predictions.
DOI: 10.5281/zenodo.13269783
title: Please Use Version 3

description: Please use the Version 3
DOI: 10.5281/zenodo.13270459
title: Gene Enhancer Predictions in C2C12 (Mouse Myoblast)

description: This file contains the complete enhancer prediction output of the analysis done in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

using the Activity by Contact Model following the pipeline described here: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

To be used in this analysis, a genomewide Hi-C interaction matrix was generated with Juicer  v1.6, expression counts for each gene were generated with STAR v2.7.10b and Rsubread v2.8.2, and the sequence alignment maps of ATAC-seq and H3K27ac ChIP-seq were generated with NextGenMap v0.5.5, all using raw sequencing reads downloaded from SRA: Hi-C (SRR16220088), RNA-seq (SRR074113 and SRR074114), ATAC-seq (SRR2999996) and H3K27ac ChIP-seq (SRR358589, SRR358590, and SRR358591).

The chromosome coordinates are of the GRCm38 - mm10 assembly, and the gene IDs are from ENSEMBL annotation.

Please use the Version 3, and for more information please refer to our publication that used these enhancer predictions.
DOI: 10.6084/m9.figshare.28638467
title: SERUM ELISA WT mRNA Pfizer NEW UTRs.xlsx

description: ELISA for anti-S-protein antibody on sera from vaccinated mice
DOI: 10.15468/dl.j4wd89
title: Occurrence Download

description: A dataset containing 12959 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelostoma rapunculi (Lepeletier, 1841)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12959 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020130-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10671301
title: C2C12 WFS1 CHIPseq Peaks

description: 30 and 36 cycles combined WFS1 peaks used in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

Genome assembly is mm10, MACS2 software was used to call the peaks.

For more information please refer to our publication that used these enhancer predictions titled:

MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers

 

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P29713-B28, P32512-B and P36503-B] to Roland Foisner and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28].
DOI: 10.5281/zenodo.10671302
title: C2C12 WFS1 CHIPseq Peaks

description: 30 and 36 cycles combined WFS1 peaks used in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

Genome assembly is mm10, MACS2 software was used to call the peaks.

For more information please refer to our publication that used these enhancer predictions titled:

MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers

 

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P29713-B28, P32512-B and P36503-B] to Roland Foisner and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28].
DOI: 10.5281/zenodo.13270435
title: Gene Enhancer Predictions in C2C12 (Mouse Myoblast)

description: This file contains the complete enhancer prediction output of the analysis done in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

using the Activity by Contact Model following the pipeline described here: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

To be used in this analysis, a genomewide Hi-C interaction matrix was generated with Juicer  v1.6, expression counts for each gene were generated with STAR v2.7.10b and Rsubread v2.8.2, and the sequence alignment maps of ATAC-seq and H3K27ac ChIP-seq were generated with NextGenMap v0.5.5, all using raw sequencing reads downloaded from SRA: Hi-C (SRR16220088), RNA-seq (SRR074113 and SRR074114), ATAC-seq (SRR2999996) and H3K27ac ChIP-seq (SRR358589, SRR358590, and SRR358591).

The chromosome coordinates are of the GRCm38 - mm10 assembly, and the gene IDs are from ENSEMBL annotation.

 

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P29713-B28, P32512-B and P36503-B] to Roland Foisner and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28].

 

For more information please refer to our publication that used these enhancer predictions titled:

MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers
DOI: 10.5281/zenodo.13270436
title: Gene Enhancer Predictions in C2C12 (Mouse Myoblast)

description: This file contains the complete enhancer prediction output of the analysis done in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

using the Activity by Contact Model following the pipeline described here: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

To be used in this analysis, a genomewide Hi-C interaction matrix was generated with Juicer  v1.6, expression counts for each gene were generated with STAR v2.7.10b and Rsubread v2.8.2, and the sequence alignment maps of ATAC-seq and H3K27ac ChIP-seq were generated with NextGenMap v0.5.5, all using raw sequencing reads downloaded from SRA: Hi-C (SRR16220088), RNA-seq (SRR074113 and SRR074114), ATAC-seq (SRR2999996) and H3K27ac ChIP-seq (SRR358589, SRR358590, and SRR358591).

The chromosome coordinates are of the GRCm38 - mm10 assembly, and the gene IDs are from ENSEMBL annotation.

 

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P29713-B28, P32512-B and P36503-B] to Roland Foisner and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28].

 

For more information please refer to our publication that used these enhancer predictions titled:

MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers
DOI: 10.15468/dl.pdh793
title: Occurrence Download

description: A dataset containing 52055572 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 52055572 records from 3122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020115-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b7fwuk
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prunus serotina",
 "HasCoordinate is true",
 "Country is Luxembourg"
 ]
}

 The dataset includes 86 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005004-251009101135966/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.30327880
title: Data and figures for: Crustal magnetic control of the martian oxygen corona

description: This dataset contains the figures and associated data that support the paper <i>“Crustal Magnetic Control of the Martian Oxygen Corona.”</i>
DOI: 10.15156/bio/sh1131856.10fu
title: SH1131856.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1131858.10fu
title: SH1131858.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.