Datasets of variants from DNAseq and RNAseq in pigs

DOI

These datasets correspond to .vcf files (variants calling files) obtained from DNAseq and RNAseq in different tissues in pigs. Dataset1 corresponds to data generated from reciprocal crosses used to study genomic imprinting in hypothalamus and muscle in 1day piglets. Dataset2 corresponds to data generated from reciprocal crosses used to study genomic imprinting in placenta in 110days post-fertilization fetuses. Metadata of individuals (pedigree) are also available.

  • Dataset1_DNAseq_variants_final.vcf.gz corresponds to variants identified from blood DNA in both parents and offspring (n=14) only on autosomes;
  • Dataset1_RNAseq_hypothalamus_variants_final.vcf.gz corresponds to variants identified from hypothalamus RNA in offpsring (n=9) only on autosomes;
  • Dataset1_RNAseq_muscle_variants_final.vcf.gz corresponds to variants identified from muscle RNA in offpsring (n=9) only on autosomes;
  • Dataset1_Metadata_Pedigree.txt corresponds to pedigree information and samples ID in Dataset1;
  • Dataset2_DNAseq_variants_final.vcf.gz corresponds to variants reconstructed from DNA in both parents and offspring (n=71) only on autosomes;
  • Dataset2_RNAseq_placenta_variants_final.vcf.gz corresponds to variants identified from placenta RNA in fetuses (n=54) only on autosomes;
  • Dataset2_Metadata_Pedigree.txt corresponds to pedigree information and samples ID in Dataset2.

Both datasets are used in the preprint https://doi.org/10.1101/2025.03.09.642261

Identifier
DOI https://doi.org/10.57745/RF5PUT
Related Identifier IsCitedBy https://doi.org/10.1101/2025.03.09.642261
Metadata Access https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.57745/RF5PUT
Provenance
Creator Demars, Julie ORCID logo
Publisher Recherche Data Gouv
Contributor Demars, Julie; INRAE; Entrepôt-Catalogue Recherche Data Gouv
Publication Year 2025
Funding Reference Agence nationale de la recherche ANR-18-CE20-0018 ; Operational program ERDF-FSE MIDI-PYRENEES ET GARONNE 2014-2020 SeqOccIn project ; Agence nationale de la recherche ANR-09-GENM005 ; Agence nationale de la recherche ANR-20-CE20-0020
Rights etalab 2.0; info:eu-repo/semantics/restrictedAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess false
Contact Demars, Julie (INRAE)
Representation
Resource Type Dataset
Format application/x-gzip; text/plain
Size 304717666; 1004; 255076494; 159100940; 414113962; 3051; 215480498
Version 1.0
Discipline Agriculture, Forestry, Horticulture; Agricultural Sciences; Agriculture, Forestry, Horticulture, Aquaculture; Agriculture, Forestry, Horticulture, Aquaculture and Veterinary Medicine; Basic Biological and Medical Research; Biology; Life Sciences; Omics