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An ATAC-seq atlas of chromatin accessibility in mouse tissues

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May 20, 2019

Chuanyu Liu, Mingyue Wang, Xiaoyu Wei, Liang Wu, Jiangshan Xu, Xi Dai, Jun Xia, Mengnan Cheng, Yue Yuan, Pengfan Zhang, Jiguang Li, Taiqing Feng, Ao Chen, Wenwei Zhang, Fang Chen, Zhouchun Shang, Xiuqing Zhang, Brock A. Peters & Longqi Liu

Scientific Data 6, Article number: 65 (2019)

An ATAC-seq atlas of chromatin accessibility in mouse tissues

Abstract

The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics in multiple species. A comprehensive reference of ATAC-seq datasets for mammalian tissues is important for the understanding of regulatory specificity and developmental abnormality caused by genetic or environmental alterations. Here, we report an adult mouse ATAC-seq atlas by producing a total of 66 ATAC-seq profiles from 20 primary tissues of both male and female mice. The ATAC-seq read enrichment, fragment size distribution, and reproducibility between replicates demonstrated the high quality of the full dataset. We identified a total of 296,574 accessible elements, of which 26,916 showed tissue-specific accessibility. Further, we identified key transcription factors specific to distinct tissues and found that the enrichment of each motif reflects the developmental similarities across tissues. In summary, our study provides an important resource on the mouse epigenome and will be of great importance to various scientific disciplines such as development, cell reprogramming, and genetic disease.

Design Type(s) epigenetic modification identification objective • organism part comparison design
Measurement Type(s) assay for transposase-accessible chromatin using sequencing
Technology Type(s) next generation DNA sequencing
Factor Type(s) technical replicate • biological replicate • animal body part
Sample Characteristic(s) Mus musculus • adrenal gland • brain • cerebellum • visceral abdominal adipose tissue • brown adipose tissue • adipose tissue • heart • kidney • liver • lung • ovary • pancreas • skeletal muscle tissue • spleen • thymus • uterus • bladder organ • large intestine • small intestine • stomach

More info at: https://www.nature.com/articles/s41597-019-0071-0

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