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BarkBase: Epigenomic Annotation of Canine Genomes
Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.ORCID iD: 0000-0001-5770-0989
Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
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2019 (English)In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 6, article id 433Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
MDPI , 2019. Vol. 10, no 6, article id 433
Keywords [en]
dog, expression, genome, annotation, ATAC-seq, RNA-seq, epigenomic, canine, comparative
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-390646DOI: 10.3390/genes10060433ISI: 000473797000028PubMedID: 31181663OAI: oai:DiVA.org:uu-390646DiVA, id: diva2:1343781
Funder
NIH (National Institute of Health), 5R24OD018250Available from: 2019-08-19 Created: 2019-08-19 Last updated: 2019-08-19Bibliographically approved

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Genereux, Diane P.Morrill, KathleenSharp, Claire R.Lindblad-Toh, KerstinKarlsson, Elinor K.
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