cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14865689
title: Custom genome used in Rouco et al. 2024/2025

description: This dataset contains the custom genomes generated to analyse sequencing data in the manuscript titled "Temporal constraints on enhancer usage shape the regulation of limb gene transcription" by Rouco et al. 2024_2025. For more information see Materials and Methods section. 

The main customized genome and index used across the manuscript were generated based on the GRCm39/mm39 (Cunningham et al., 2022) incorporating the dmCherry-P2A-CRE and floxed-SV40pASTOP-EYFP cassettes as artificial chromosomes, therefore we termed it as GRCmm39/ mm39_dsmCherry_P2A_CRE_EYFP genome:

mm39_dsmCherry_P2A_CRE_EYFP.fa

mm39_dsmCherry_P2A_CRE_EYFP.fa.fai

These files were used to build a custom reference for different downstream analyses using the following pipelines:CellRanger: cellranger_mm39_dsmCherry_P2A_CRE_EYFP.sh  

Bowtie2: bowtie2_mm39_dsmCherry_P2A_CRE_EYFP.sh

Star: star_mm39_dsmCherry_P2A_CRE_EYFP.sh

For annotation, GTF files sourced from ENSEMBL GRCm39 release 104 (Cunningham et al., 2022) were used, with a filtering process applied to exclude read-through/overlapping transcripts. Only transcripts annotated as 'protein-coding' for their respective genes were retained, while those flagged as 'retained_intron', 'nonsense-mediated decay', etc., were discarded. This filtration aimed to retain only unambiguous exons, mitigating potential quantitative biases during data analysis conducted using STAR/Cufflinks (Amandio et al., 2016).

mergeOverlapGenesOfFilteredTranscriptsOfMus_musculus.GRCm39.104_ExonsOnly_UCSC_dsmCherry_P2A_CRE_EYFP.gtf

The second customized genome and index used in this manuscript, for precise genotype characterization, was generated based on the GRCm39/mm39 (Cunningham et al., 2022) incorporating the dmCherry-P2A-CRE cassette at the Shox2 locus, therefore we termed it as GRCmm39/ mm39_Shox2_dsmCherry_P2A_CRE_bGHpA_KI genome:

mm39_Shox2_dsmCherry_P2A_CRE_bGHpA_KI.fa

mm39_Shox2_dsmCherry_P2A_CRE_bGHpA_KI.fa.fai

These files were used to build a custom reference for different downstream analyses using the following pipeline:

bowtie2_mm39_Shox2_dsmCherry_P2A_CRE_bGHpA_KI.sh

The following GTF with the shifted coordinates accounting for the insertion of the cassette was also created:

shifted_completed_mm39_Shox2_dsmCherry_P2A_CRE_KI.gtf

Files with shifted coordinates following the pipeline described in: https://github.com/lldelisle/howCanYou/tree/main/NGS/mutant_genome#shift-annotations-to-work-on-your-mutant-genome
DOI: 10.15468/dl.7hk44u
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Vigna ambacensis var. pubigera (Baker) Maréchal, Mascherpa & Stainier"
 ]
}

 The dataset includes 47 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000369-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a7tz9k
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Stelis dimidia (Luer) Karremans"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000370-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2dwx5
title: Occurrence Download

description: A dataset containing 11217 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-173.274 -62.37058,-21.4755 -62.37058,-21.4755 71.73338,-173.274 71.73338,-173.274 -62.37058))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is New York",
 "TaxonKey is Ailanthus altissima (Mill.) Swingle"
 ]
}

 The dataset includes 11217 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000372-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kuwrq3
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Vigna ambacensis Welw."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000371-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s9mxyp
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diomedea nigripes Audubon, 1839",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000373-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fyxs8v
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Vigna benuensis Pasquet & Maréchal"
 ]
}

 The dataset includes 41 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000374-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14469/hpc/14832
title: Borate-Catalysed Direct Amidation Reactions of Coordinating Substrates. Kinetic Data

description: kinetic data used to plot the graphs in Schemes 1 and 2
DOI: 10.14469/hpc/14884
title: Finding Aid for Borate-Catalysed Direct Amidation Reactions of Coordinating Substrates. NMR Data.
DOI: 10.15468/dl.sryedb
title: Occurrence Download

description: A dataset containing 236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paraplagusia japonica (Temminck & Schlegel, 1846)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 236 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000375-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zuwpju
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plagusia japonica Temminck & Schlegel, 1846",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000377-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15161/oar.it/211427
title: Carta Geologica d'Italia alla scala 1:50.000, F. 489 Marsico Nuovo

description: Foglio geologico alla scala 1:50.000 basato su rilevamenti alla scala 1:10.000 (eseguiti tra il 1997 e il 2000) comprensivo di legenda, schemi a cornice, sezioni geologiche.
DOI: 10.15468/dl.87qncv
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudopleuronectes herzensteini (Jordan & Snyder, 1901)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 130 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000378-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25318/3510003201-eng
title: Adult criminal courts, guilty cases by length of custody

description: Adult criminal courts, type of guilty finding by offence, age and sex of accused and length of custody, Canada, provinces, territories, ten jurisdictions and eight jurisdictions, five years of data.
DOI: 10.15468/dl.wex6zg
title: Occurrence Download

description: A dataset containing 705 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Paraguay",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is one of (Canindeyu Department, Canindeyu, Caaguazu, Caazapa/Itapua, Alto Parana, Alto Parana Department)",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 705 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000380-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.x7my0unj
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (311 records)
DOI: 10.25318/3510003201-fra
title: Tribunaux de juridiction criminelle pour adultes, causes avec condamnation selon la durée du placement sous garde

description: Tribunaux de juridiction criminelle pour adultes, type de condamnation selon l'infraction, l'âge et le sexe de l'accusé et la durée du placement sous garde, Canada, provinces, territoires, dix secteurs de compétence et huit secteurs de compétence, cinq années de données.
DOI: 10.15468/dl.uyuty2
title: Occurrence Download

description: A dataset containing 51408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus castaneifolia C.A.Mey., Quercus cerris L., Quercus libani G.Olivier, Quercus look Kotschy)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1900",
 "Year is less than or equal to 2024",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 51408 records from 319 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000379-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.2908/tag00059
title: Selling prices of soft wheat
title: Prix de vente de blé tendre
title: Verkaufspreise für Weichweizen

description: Corresponds to the absolute prices of the products. Expressed in euro per 100 kilo. Prices are net of VAT.
description: Entspricht den absoluten Preisen der Produkte. Ausgedrückt in Euro pro 100 Kilo. Die Preise verstehen sich zuzüglich Mehrwertsteuer.
description: Correspond aux prix absolus des produits. Exprimé en euros pour 100 kilos. Les prix sont hors TVA.
DOI: 10.2908/tag00060
title: Selling prices of barley
title: Prix de vente d'orge
title: Verkaufspreise für Gerste

description: Corresponds to the absolute prices of the products. Expressed in euro per 100 kilo. Prices are net of VAT.
description: Entspricht den absoluten Preisen der Produkte. Ausgedrückt in Euro pro 100 Kilo. Die Preise verstehen sich zuzüglich Mehrwertsteuer.
description: Correspond aux prix absolus des produits. Exprimé en euros pour 100 kilos. Les prix sont hors TVA.
DOI: 10.2908/tag00061
title: Selling prices of oats
title: Prix de vente d'avoine
title: Verkaufspreise für Hafer

description: Corresponds to the absolute prices of the products. Expressed in euro per 100 kilo. Prices are net of VAT.
description: Entspricht den absoluten Preisen der Produkte. Ausgedrückt in Euro pro 100 Kilo. Die Preise verstehen sich zuzüglich Mehrwertsteuer.
description: Correspond aux prix absolus des produits. Exprimé en euros pour 100 kilos. Les prix sont hors TVA.
DOI: 10.2908/tag00062
title: Selling prices of maize
title: Prix de vente de mais
title: Verkaufspreise für Mais

description: Corresponds to the absolute prices of the products. Expressed in euro per 100 kilo. Prices are net of VAT.
description: Entspricht den absoluten Preisen der Produkte. Ausgedrückt in Euro pro 100 Kilo. Die Preise verstehen sich zuzüglich Mehrwertsteuer.
description: Correspond aux prix absolus des produits. Exprimé en euros pour 100 kilos. Les prix sont hors TVA.
DOI: 10.2908/tag00063
title: Selling prices of main crop potatoes
title: Prix de vente des pommes terre de consommation
title: Verkaufspreise für Speisekartoffeln

description: Entspricht den absoluten Preisen der Produkte. Ausgedrückt in Euro pro 100 Kilo. Die Preise verstehen sich zuzüglich Mehrwertsteuer.
description: Correspond aux prix absolus des produits. Exprimé en euros pour 100 kilos. Les prix sont hors TVA.
description: Corresponds to the absolute prices of the products. Expressed in euro per 100 kilo. Prices are net of VAT.
DOI: 10.2908/tag00064
title: Selling prices of sugar beet (unit value)
title: Prix de vente des betteraves sucrières (valeur unitaire)
title: Verkaufspreise für Zuckerrüben (Durchschnittserlös)

description: Correspond aux prix absolus des produits. Exprimé en euros pour 100 kilos. Les prix sont hors TVA.
description: Entspricht den absoluten Preisen der Produkte. Ausgedrückt in Euro pro 1000 Kilo. Die Preise verstehen sich zuzüglich Mehrwertsteuer.
description: Corresponds to the absolute prices of the products. Expressed in euro per 1000 kilo. Prices are net of VAT.
DOI: 10.2908/tag00065
title: Selling prices of calves
title: Prix de vente des veaux
title: Verkaufspreise für Kälber

description: Correspond aux prix absolus de vente de la production animale. Exprimé en euros pour 100 kilos de poids vif. Les prix sont hors TVA.
description: Entspricht den absoluten Verkaufspreisen der Tierproduktion. Ausgedrückt in Euro pro 100 Kilo Lebendgewicht. Die Preise verstehen sich zuzüglich Mehrwertsteuer.
description: Corresponds to the absolute prices of animal production. Expressed in euro per 100 kilo live weight. Prices are net of VAT.
DOI: 10.15468/dl.pp97ge
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Makaira mazara (Jordan & Snyder, 1901)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000383-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zr7exn
title: Occurrence Download

description: A dataset containing 11853 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "DatasetKey is one of (Galapagos Subtidal Biodiversity, NMNH Extant Specimen Records (USNM, US), Museum of Comparative Zoology, Harvard University, LACM Echinoderms, Evaluación submareal de los bajos “EL ACUARIO” y “RABO DEL VIEJO” de la Reserva Marina El Pelado, Provincia de Santa Elena - 2023, Macroinvertebrate groups found on deep-sea volcanic habitats in the Galapagos Marine Reserve in the Eastern Tropical Pacific Ocean: Echinoderms, Caracterización de la Biodiversidad Microbiológica y de Invertebrados de la Reserva Marina \"El Pelado\" a escala Taxonómica, Metabolómica y Metagenómica para su uso en salud humana y animal, MONITOREO DE BIODIVERSIDAD DEL INTERMAREAL ROCOSO Reservas Marinas: El Pelado, Bajo Copé y Cantagallo – Machalilla, FKt230918 expedition – Vertical Reef of the Galapagos)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Echinodermata"
 ]
}

 The dataset includes 11853 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000381-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nhn92j
title: Occurrence Download

description: A dataset containing 7536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is United States of America",
 "Geometry POLYGON((-109.42771 34.97639,-96.50199 34.97639,-96.50199 42.15679,-109.42771 42.15679,-109.42771 34.97639))",
 "HasGeospatialIssue is false",
 "TaxonKey is Orchidaceae"
 ]
}

 The dataset includes 7536 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000382-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wudnam
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aeschynomene brasiliana (Poir.) DC.",
 "Country is Australia",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 7 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000384-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hqma5x
title: Occurrence Download

description: A dataset containing 2635 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "DatasetKey is one of (Galapagos Subtidal Biodiversity, Colección Marina Estación Científica Charles Darwin, Caracterización de la Biodiversidad Microbiológica y de Invertebrados de la Reserva Marina \"El Pelado\" a escala Taxonómica, Metabolómica y Meta genómica para su uso en salud humana y animal, Macroinvertebrate groups found on deep-sea volcanic habitats in the Galapagos Marine Reserve in the Eastern Tropical Pacific Ocean: Porifera, Type locality distributions from the World Register of Marine Species, NMNH Extant Specimen Records (USNM, US), Naturalis Biodiversity Center (NL) - Porifera, Vulnerable marine ecosystems in the South Pacific Ocean region, NOAA Deep-Sea Coral Research and Technology Program)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Porifera"
 ]
}

 The dataset includes 2635 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000385-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25318/3510017601-eng
title: Key indicator results and absolute change for preliminary quarterly data, adult criminal court and youth court

description: Preliminary quarterly key indicator results and year-over-year absolute change (refers to the simple difference in the indicator over two periods of time (new-old)) for adult criminal courts and youth courts, by offence and sex of accused, for all reporting provinces and territories.
DOI: 10.15468/dl.4tycjm
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Makaira nigricans Lacepède, 1802",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000387-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25318/3510017601-fra
title: Résultats et variation absolue des indicateurs clés pour les données trimestrielles provisoires, tribunaux de juridiction criminelle pour adultes et tribunaux de la jeunesse

description: Résultats et différences absolues (fait référence à la simple différences dans l’indicateur sur deux périodes de temps (nouvelle – antérieure)) d’année en année des indicateurs clés pour les données trimestrielles provisoires des tribunaux de juridiction criminelle pour adultes et les tribunaux de la jeunesse, par infraction et le sexe de l’accusé, pour toutes les provinces et territoires déclarantes.
DOI: 10.15156/bio/sh0196896.10fu
title: SH0196896.10FU

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/sh0196897.10fu
title: SH0196897.10FU

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/sh0196898.10fu
title: SH0196898.10FU

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.