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Genes (Basel). 2019 Jun 7;10(6). pii: E433. doi: 10.3390/genes10060433.

BarkBase: Epigenomic Annotation of Canine Genomes.

Author information

1
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. kmegq@broadinstitute.org.
2
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. genereux@broadinstitute.org.
3
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. jphekman@broadinstitute.org.
4
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. swofford@broadinstitute.org.
5
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. jturner@broadinstitute.org.
6
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. jjohnson@broadinstitute.org.
7
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. jalonso@broadinstitute.org.
8
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. xue.li2@umassmed.edu.
9
Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA. xue.li2@umassmed.edu.
10
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. brittney.logan@umassmed.edu.
11
Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA. brittney.logan@umassmed.edu.
12
Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA. lja2@cornell.edu.
13
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. perloski@broadinstitute.org.
14
School of Veterinary and Life Sciences, College of Veterinary Medicine, Murdoch University, Perth, Murdoch, WA 6150, Australia. C.Sharp@murdoch.edu.au.
15
Departament de Medicina i Cirurgia Animals Veterinary School, Universitat Autonoma de Barcelona, 08193 Barcelona, Spain. Lluis.Ferrer@tufts.edu.
16
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. kersli@broadinstitute.org.
17
Science for Life Laboratory, Department of Medical Biochemistry & Microbiology, Uppsala University, 751 23 Uppsala, Sweden. kersli@broadinstitute.org.
18
Baker Institute for Animal Health and Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA. meyerswallen@gmail.com.
19
School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. hoffm018@upenn.edu.
20
Cummings School of Veterinary Medicine, Tufts University, Grafton, MA 01536, USA. hoffm018@upenn.edu.
21
Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. elinor.karlsson@umassmed.edu.
22
Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA. elinor.karlsson@umassmed.edu.
23
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA. elinor.karlsson@umassmed.edu.

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.

KEYWORDS:

ATAC-seq; RNA-seq; annotation; canine; comparative; dog; epigenomic; expression; genome

PMID:
31181663
DOI:
10.3390/genes10060433
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