Cited by 2,496Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

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

Open access
Corces, M Ryan, Trevino, Alexandro E, Hamilton, Emily G, Greenside, Peyton G, Sinnott-Armstrong, Nicholas A, Vesuna, Sam, Satpathy, Ansuman T, Rubin, Adam J +14 more·2017·Nature Methods

Published version of a preprint

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.

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  • ATAC-seq of Lymph- Ery- cKit+ populations uncovered alterations in chromatin accessibility in compound mutant cells compared with nonleukemic cells.

    “improved transposase-accessible chromatin by sequencing (ATAC-seq; ref. 36) of Lymph- Ery- cKit+ populations (sorted as in Fig. 4C and D) uncovered alterations in chromatin accessibility in compound mutant cells compared with nonleukemic (combined WT, UREHET, Tet2HET, and Tet2KO) cells”

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Authors
Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., Kathiria, A., Cho, S. W., Mumbach, M. R., Carter, A. C., Kasowski, M., Orloff, L. A., Risca, V. I., Kundaje, A., Khavari, P. A., Montine, T. J., Greenleaf, W. J., & Chang, H. Y.
Affiliations
  • Stanford Medicine (US)
  • Stanford University (US)
  • Chan Zuckerberg Biohub San Francisco (US)
Corresponding author
  • Greenleaf, William J
  • Chang, Howard Y
Venue
Nature Methods
Published
2017-08-28
Volume
14
Issue
10
Pages
959-962
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W2750416916
Cited by
2,496
References
6
Citations by year
2026: 290 · 2025: 386 · 2024: 385 · 2023: 374 · 2022: 341 · 2021: 319 · 2020: 233 · 2019: 120 · 2018: 43 · 2017: 2 · 2012: 1
FWCI
44.48
Type
journal article
Language
en
Open access
Locations
  • Nature Methods (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Scholarworks@UNIST (Ulsan National Institute of Science and Technology) (submittedVersion)
Funders
  • National Science Foundation (P50 AG047366)
  • National Institutes of Health (NIH P50, AG053959, AG047366, P50-HG007735, NS062684, HG007735)
  • National Defense Science and Engineering Graduate (32 CFR 168a, CFR 168a)
  • National Institute on Aging (AG047366, P50AG047366, NIH P50, AG053959, RF1AG053959)
  • National Human Genome Research Institute (UM1HG009436, P50HG007735, T32HG000044)
  • National Cancer Institute (R25CA180993, P30CA124435)
  • National Institute of Allergy and Infectious Diseases (U19AI057266)
  • National Institute of Neurological Disorders and Stroke (P50NS062684)
  • U.S. National Library of Medicine (T15LM007033)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
signal-to-background ratio, frozen tissue, archival tissue, human brain structure, tissue context
MeSH terms
Animals, Brain, Cell Line, DNA, Erythrocytes, Freezing, Humans, Specimen Handling, Thyroid Neoplasms, Keratinocytes, Gene Expression Regulation, Enzymologic, Genome, Transposases, Self-Sustained Sequence Replication, Mice, Genome-Wide Association Study

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