Journal article
BarkBase: Epigenomic annotation of canine genomes
Genes, Vol.10(6)
2019
Abstract
Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans.
Details
- Title
- BarkBase: Epigenomic annotation of canine genomes
- Authors/Creators
- K. Megquier (Author/Creator) - Broad InstituteD.P. Genereux (Author/Creator) - Broad InstituteJ. Hekman (Author/Creator) - Broad InstituteR. Swofford (Author/Creator) - Broad InstituteJ. Turner-Maier (Author/Creator) - Broad InstituteJ. Johnson (Author/Creator) - Broad InstituteJ. Alonso (Author/Creator) - Broad InstituteX. Li (Author/Creator) - University of Massachusetts Chan Medical SchoolK. Morrill (Author/Creator) - University of Massachusetts Chan Medical SchoolL.J. Anguish (Author/Creator) - Cornell UniversityM. Koltookian (Author/Creator) - Broad InstituteB. Logan (Author/Creator) - University of Massachusetts Chan Medical SchoolC.R. Sharp (Author/Creator) - Murdoch UniversityL. Ferrer (Author/Creator) - Universitat Autònoma de BarcelonaK. Lindblad-Toh (Author/Creator) - Science for Life LaboratoryV.N. Meyers-Wallen (Author/Creator) - Cornell UniversityA. Hoffman (Author/Creator) - University of PennsylvaniaE.K. Karlsson (Author/Creator) - University of Massachusetts Chan Medical School
- Publication Details
- Genes, Vol.10(6)
- Publisher
- MDPI
- Identifiers
- 991005542214707891
- Copyright
- © 2019 by the authors. Licensee MDPI, Basel, Switzerland.
- Murdoch Affiliation
- School of Veterinary and Life Sciences
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.189 Genome Studies
- 1.189.310 Population Genetics
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics