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Related Experiment Video

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Reusable Single Cell for Iterative Epigenomic Analyses

Reusable Single Cell for Iterative Epigenomic Analyses

Published on: February 11, 2022

BarkBase: Epigenomic Annotation of Canine Genomes.

Kate Megquier¹, Diane P Genereux², Jessica Hekman³

¹Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. kmegq@broadinstitute.org.

|June 12, 2019

Summary

Researchers created BarkBase, a canine epigenomic resource, to better understand dog genetics and complex diseases like cancer. This new database provides crucial canine-specific genomic data for improved disease research and comparative studies.

Keywords:

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

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Area of Science:

Genomics
Comparative Biology
Canine Genetics

Background:

Dogs serve as valuable natural models for studying complex diseases, including cancer.
Accurate genomic annotation of regulatory elements in healthy canine tissues is essential for identifying disease-causing genetic variants.
Current canine genetic research often relies on remapped human or mouse genome annotations, which may miss dog-specific genomic features.

Purpose of the Study:

To introduce BarkBase, a comprehensive canine epigenomic resource.
To provide dog-specific genomic data for regulatory elements across various tissues and developmental stages.
To facilitate comparative genomic studies between dogs and humans.

Main Methods:

Collected RNA sequencing and whole genome sequencing data from 27 adult canine tissues and four embryonic time points.
Utilized Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to identify open chromatin regions.
Incorporated biological replicates to enhance the accuracy of transcript and gene expression analysis.

Main Results:

BarkBase offers extensive epigenomic data for 27 adult tissues and embryonic samples.
The resource includes RNA sequencing, whole genome sequencing, and ATAC-seq data.
Data is available in user-friendly formats with a visual browser for easy access and analysis.

Conclusions:

BarkBase is a powerful new resource for canine genetic research, offering dog-specific epigenomic information.
The resource supports the identification of candidate causal variants and the design of functional studies for canine diseases.
BarkBase enables robust comparative studies, advancing our understanding of both canine and human health and disease genetics.