An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

M Ryan Corces; Alexandro E Trevino; Emily G Hamilton; Peyton G Greenside; Nicholas A Sinnott-Armstrong; Sam Vesuna; Ansuman T Satpathy; Adam J Rubin; Kathleen S Montine; Beijing Wu; Arwa Kathiria; Seung Woo Cho; Maxwell R Mumbach; Ava C Carter; Maya Kasowski; Lisa A Orloff; Viviana I Risca; Anshul Kundaje; Paul A Khavari; Thomas J Montine; William J Greenleaf; Howard Y Chang

doi:10.1038/nmeth.4396

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Nat Methods. 2017 Oct;14(10):959-962. doi: 10.1038/nmeth.4396. Epub 2017 Aug 28.

Authors

M Ryan Corces^{1

2}, Alexandro E Trevino^{1

3

4}, Emily G Hamilton⁵, Peyton G Greenside^{3

6}, Nicholas A Sinnott-Armstrong³, Sam Vesuna⁴, Ansuman T Satpathy^{1

7}, Adam J Rubin², Kathleen S Montine⁷, Beijing Wu³, Arwa Kathiria³, Seung Woo Cho^{1

2}, Maxwell R Mumbach^{1

3}, Ava C Carter^{1

2}, Maya Kasowski^{1

7}, Lisa A Orloff⁸, Viviana I Risca³, Anshul Kundaje^{3

9}, Paul A Khavari², Thomas J Montine⁷, William J Greenleaf^{1

3

10}, Howard Y Chang^{1

2}

Affiliations

¹ Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.
² Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA.
³ Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
⁴ Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA.
⁵ Program in Cancer Biology, Stanford University School of Medicine, Stanford, California, USA.
⁶ Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, USA.
⁷ Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.
⁸ Department of Otolaryngology Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, USA.
⁹ Department of Computer Science, Stanford University, Stanford, California, USA.
¹⁰ Chan Zuckerberg Biohub, San Francisco, California, USA.

Abstract

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

MeSH terms

Animals
Brain
Cell Line
DNA / genetics*
Erythrocytes
Freezing*
Gene Expression Regulation, Enzymologic
Genome*
Genome-Wide Association Study
Humans
Keratinocytes
Mice
Self-Sustained Sequence Replication
Specimen Handling / methods*
Thyroid Neoplasms
Transposases / metabolism

Substances

DNA
Transposases

Abstract

MeSH terms

Substances

Grants and funding