ATAC Sequencing Protocol For Cryopreserved Mammalian Cells

Juan Manuel Caravaca; Monika Mehta; Sujatha Gowda; Bao Tran

doi:10.21769/BioProtoc.4294

ATAC Sequencing Protocol For Cryopreserved Mammalian Cells

Bio Protoc. 2022 Jan 20;12(2):e4294. doi: 10.21769/BioProtoc.4294.

Authors

Juan Manuel Caravaca¹, Monika Mehta¹, Sujatha Gowda¹, Bao Tran¹

Affiliation

¹ Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Abstract

ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) is a powerful method to evaluate chromatin accessibility and nucleosome positioning at a genome-wide scale. This assay uses a hyperactive Tn5 transposase, to simultaneously cut open chromatin and insert adapter sequences. After sequencing, the reads generated through this technique are generally indicative of transcriptional regulatory elements that are located in accessible chromatin. This method was originally developed by Buenrostro et al. (2013), and since then it has been improved by the same authors several times, until their last update called OMNI ATAC-seq ( Corces et al., 2017 ). Here, we describe an ATAC-seq protocol based on the OMNI-ATAC method, with a special focus on the initial steps of thawing cryopreserved cells, and the final steps of library purification using magnetic beads. This protocol can be of interest for laboratories working in a fast-paced environment. Graphic abstract: Flowchart of the protocol.

Keywords: ATAC-seq; Chromatin accessibility; Cryopreserved cells; Genome wide; Nucleosome positioning; Transposase.