Academic Program
NeuroscienceUMass Chan Affiliations
Graduate School of Biomedical SciencesProgram in Molecular Medicine
Program in Bioinformatics and Integrative Biology
Document Type
Journal ArticlePublication Date
2019-06-07Keywords
ATAC-seqRNA-seq
annotation
canine
comparative
dog
epigenomic
expression
genome
Animal Experimentation and Research
Bioinformatics
Computational Biology
Genetic Phenomena
Genetics and Genomics
Genomics
Metadata
Show full item recordAbstract
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.Source
Genes (Basel). 2019 Jun 7;10(6). pii: genes10060433. doi: 10.3390/genes10060433. Link to article on publisher's site
DOI
10.3390/genes10060433Permanent Link to this Item
http://hdl.handle.net/20.500.14038/44375PubMed ID
31181663Notes
Full author list omitted for brevity. For the full list of authors, see article.
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Rights
© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Distribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.3390/genes10060433
Scopus Count
Except where otherwise noted, this item's license is described as © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).