@article{ff5d16a11c4a4c5db4d1567232e5b2f4,
title = "Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinoma",
abstract = "Single-cell ATAC sequencing using combinatorial indexing (sciATAC-seq) enables the identification of chromatin accessibility profiles at single-cell resolution with a dual-barcoding approach during transposition and library construction. Unlike commercial droplet-based approaches, sciATAC-seq is a cost-effective, extensible strategy that permits flexibility in the experimental scale via multiplexed barcoding across samples or perturbations. In contrast, droplet-based approaches have higher cell recovery and may be advantageous when cell input is limited. The step-by-step sciATAC-seq protocol described here is amenable to diverse cell types and fixed samples. For complete details on the use and execution of this protocol, please refer to LaFave et al. (2020).",
keywords = "Cancer, Genomics, Molecular Biology, Sequencing, Single Cell",
author = "{Del Priore}, Isabella and Sai Ma and Jonathan Strecker and Tyler Jacks and LaFave, {Lindsay M.} and Buenrostro, {Jason D.}",
note = "Funding Information: This work was supported in part by grant P01-CA42063 from the National Institutes of Health , the Cancer Center Support (core) grant P30-CA14051 from the National Cancer Institute , and by the Howard Hughes Medical Institute (HHMI). We thank the flow cytometry cores at the Swanson Biotechnology Center, the Walk-up Sequencing Core at the Broad Institute, and the Bauer Sequencing Core at Harvard. L.M.L. is supported by a Damon Runyon Cancer Foundation postdoctoral fellowship. J.D.B. acknowledges support from the Allen Distinguished Investigator Program, through the Paul G. Allen Frontiers Group. T.J. is a Daniel K. Ludwig Scholar. Funding Information: T.J. is a member of the Board of Directors of Amgen and Thermo Fisher Scientific and a co-Founder of Dragonfly Therapeutics and T2 Biosystems. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics. T.J. is also the President of Break Through Cancer. His laboratory currently receives funding from Johnson & Johnson and Lustgarten Foundation, but these funds did not support the research described in this manuscript. J.D.B. holds patents related to ATAC-seq and scATAC-seq and serves on the Scientific Advisory Board of CAMP4 Therapeutics, seqWell, and Celsee. Funding Information: This work was supported in part by grant P01-CA42063 from the National Institutes of Health, the Cancer Center Support (core) grant P30-CA14051 from the National Cancer Institute, and by the Howard Hughes Medical Institute (HHMI). We thank the flow cytometry cores at the Swanson Biotechnology Center, the Walk-up Sequencing Core at the Broad Institute, and the Bauer Sequencing Core at Harvard. L.M.L. is supported by a Damon Runyon Cancer Foundation postdoctoral fellowship. J.D.B. acknowledges support from the Allen Distinguished Investigator Program, through the Paul G. Allen Frontiers Group. T.J. is a Daniel K. Ludwig Scholar. S.M. and L.M.L. developed and optimized the protocol. I.D.P. S.M. J.S. and L.M.L. performed the experiments. All authors contributed to experimental design. T.J. and J.D.B. supervised the research. I.D.P. S.M. J.S. L.M.L. and J.D.B. wrote the manuscript. All authors reviewed and edited the manuscript. T.J. is a member of the Board of Directors of Amgen and Thermo Fisher Scientific and a co-Founder of Dragonfly Therapeutics and T2 Biosystems. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics. T.J. is also the President of Break Through Cancer. His laboratory currently receives funding from Johnson & Johnson and Lustgarten Foundation, but these funds did not support the research described in this manuscript. J.D.B. holds patents related to ATAC-seq and scATAC-seq and serves on the Scientific Advisory Board of CAMP4 Therapeutics, seqWell, and Celsee. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2021",
month = jun,
day = "18",
doi = "10.1016/j.xpro.2021.100583",
language = "English (US)",
volume = "2",
journal = "STAR Protocols",
issn = "2666-1667",
publisher = "Cell Press",
number = "2",
}
