An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
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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”
From PU.1-Dependent Enhancer Inhibition Separates <i>Tet2</i> -Deficient Hematopoiesis from Malignant Transformation (2022) · cites this paper as [36]
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“OmniATAC–seq was performed as described previously (see the ‘HepG2, AML12 and Hepa1-6 OmniATAC-seq’ section) 89 , using 20,000– 50,00 cells obtained after FACS as input.”
Liang, J., Zhu, F., Cheng, K., Ma, N., Ma, X., Feng, Q., Xu, C., Gao, X., Wang, X., Shi, J., et al. (2023) · Advanced Materials · doi:10.1002/adma.202306158 · Cited by 84 · see citing works
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Time-resolved single-cell RNA-seq using metabolic RNA labelling
Erhard, F., Saliba, A.-E., Lusser, A., Toussaint, C., Hennig, T., Prusty, B. K., Kirschenbaum, D., Abadie, K., Miska, E. A., Friedel, C. C., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-022-00157-z · Cited by 73 · see citing works
Functional characterization of Alzheimer’s disease genetic variants in microglia
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A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility
Xu, W., Wen, Y., Liang, Y., Xu, Q., Wang, X., Jin, W., & Chen, X. (2021) · Nature Protocols · doi:10.1038/s41596-021-00583-5 · Cited by 67 · see citing works
Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs
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A human brain vascular atlas reveals diverse cell mediators of Alzheimer’s disease risk
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Single-molecule states link transcription factor binding to gene expression
Doughty, B. R., Hinks, M. M., Schaepe, J. M., Marinov, G. K., Thurm, A. R., Rios-Martinez, C., Parks, B. E., Tan, Y., Marklund, E., Dubocanin, D., et al. (2024) · Nature · doi:10.1038/s41586-024-08219-w · Cited by 42 · see citing works
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“ATAC-seq assay and libraries were prepared at the MD Anderson Epi-genomics Pro fi ling Core following the protocol as previously described 59,60 with minor modi fi cations.”
Nuclear actin structure regulates chromatin accessibility
Sen, B., Xie, Z., Thomas, M. D., Pattenden, S. G., Howard, S., McGrath, C., Styner, M., Uzer, G., Furey, T. S., & Rubin, J. (2024) · Nature Communications · doi:10.1038/s41467-024-48580-y · Cited by 35 · see citing works
Single cell epigenomic atlas of the developing human brain and organoids
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Lymphoid gene expression supports neuroprotective microglia function
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Exogenous artificial DNA forms chromatin structure with active transcription in yeast
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“Improved Assay for Transposase-Accessible Chromatin by Sequencing Improved Assay for Transposase-Accessible Chromatin by Sequencing (Omni-ATAC-seq) was performed as previously described (36), with a few alterations: FACS-purified, high viability (>90%) cKit+ cells were used.”
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“ATAC-seq CAR-T cells were sorted on CD8 (see Cell Sorting) and processed for ATAC-seq, which was carried out as previously reported (Corces et al., 2017).”
MethodSelf-citationHelios represses megakaryocyte priming in hematopoietic stem and progenitor cells
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“ATAC-seq was performed as previously described (47).”
An allostatic epigenetic memory on chromatin footprints after double-hit acute stress
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“ATAC-seq was performed as described previously 84,85 with the following modifications.”
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Enhancer grammar of liver cell types and hepatocyte zonation states
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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
- ORCID
- Corces, M Ryan
- Trevino, Alexandro E
- Hamilton, Emily G
- Sinnott-Armstrong, Nicholas A
- Vesuna, Sam
- Satpathy, Ansuman T
- Rubin, Adam J
- Montine, Kathleen S
- Cho, Seung Woo
- Mumbach, Maxwell R
- Carter, Ava C
- Kasowski, Maya
- Orloff, Lisa A
- Risca, Viviana I
- Kundaje, Anshul
- Khavari, Paul A
- Montine, Thomas J
- 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
- PMC
- PMC5623106
- 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
- green
- doi.org
- Licence
- 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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