Abstract
While methods such as the Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) enable a comprehensive characterization of regulatory DNA, additional measurements are required to characterize the multifaceted nature of eukaryotic cells. Here, we delineate the ATAC with Select Antigen Profiling by sequencing (ASAP-seq) protocol, a scalable approach to quantifying proteins via oligo-tagged antibodies alongside accessible DNA in thousands of single cells. Critically, our method utilizes a custom bridge oligo that enables the utilization of a variety of oligo-conjugated antibodies, enabling the utilization and repurposing of other commercial products. The ASAP-seq method can be completed with straightforward experimental and computational modifications existing single-cell ATAC-seq workflows but yields distinct modalities underlying complex cellular states, including estimation of protein abundance on the cell surface as well as intracellular and intranuclear factors.
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References
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Acknowledgments
C.A.L. is supported by a Stanford Science Fellowship and a Parker Institute of Cancer Immunotherapy Scholarship.
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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
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Mimitou, E.P., Smibert, P., Lareau, C.A. (2023). Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq. In: Marinov, G.K., Greenleaf, W.J. (eds) Chromatin Accessibility. Methods in Molecular Biology, vol 2611. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2899-7_13
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DOI: https://doi.org/10.1007/978-1-0716-2899-7_13
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