BarkBase : Epigenomic Annotation of Canine Genomes
Megquier, Kate (Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge.)
Genereux, Diane P. (Broad Institute of MIT and Harvard.Vertebrate Genomics)
Hekman, Jessica (Broad Institute of MIT and Harvard.Vertebrate Genomics)
Swofford, Ross (Broad Institute of MIT and Harvard.Vertebrate Genomics)
Turner-Maier, Jason (Broad Institute of MIT and Harvard.Vertebrate Genomics)
Johnson, Jeremy (Broad Institute of MIT and Harvard.Vertebrate Genomics)
Alonso, Jacob (Broad Institute of MIT and Harvard.Vertebrate Genomics)
Li, Xue (University of Massachusetts Medical School. Bioinformatics and Integrative Biology)
Morrill, Kathleen (University of Massachusetts Medical School. Bioinformatics and Integrative Biology)
Anguish, Lynne J. (Cornell University. Baker Institute for Animal Health)
Koltookian, Michele (Broad Institute of MIT and Harvard.Vertebrate Genomics)
Logan, Brittney (University of Massachusetts Medical School. Bioinformatics and Integrative Biology)
Sharp, Claire R. (Murdoch University. School of Veterinary and Life Sciences)
Ferrer i Caubet, Lluís (Universitat Autònoma de Barcelona. Departament de Medicina i Cirurgia Animals)
Lindblad-Toh, Kerstin (Uppsala University. Department of Medical Biochemistry & Microbiology)
Meyers-Wallen, Vicki N. (Cornell University. Baker Institute for Animal Health)
Hoffman, Andrew (Tufts University. Cummings School of Veterinary Medicine)
Karlsson, Elinor K. (University of Massachusetts Medical School. Program in Molecular Medicine)

Date:	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.
Note:	Número d'acord de subvenció NIH/OD/5R24OD018250
Note:	Número d'acord de subvenció NCI/5R37CA218570
Note:	Número d'acord de subvenció NIMH/R21MH109938
Note:	Número d'acord de subvenció NHGRI/1R01HG008742
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	article ; recerca ; publishedVersion
Subject:	Dog ; Expression ; Genome ; Annotation ; ATAC-seq ; RNA-seq ; Epigenomic ; Canine ; Comparative
Published in:	Genes, Vol. 10 (june 2019) , ISSN 2073-4425

DOI: 10.3390/genes10060433
PMID: 31181663

28 p, 5.4 MB

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