A protocol for simultaneous high-sensitivity genotyping and chromatin accessibility profiling in single cells.

Journal article

Single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) resolves the heterogeneity of epigenetic states across cells but does not typically capture exonic mutations, which limits our knowledge of how somatic mutations alter chromatin landscapes. Here, we present a plate-based approach coupling high-sensitivity genotyping of genomic loci with high-content scATAC-seq libraries from the same single cells. We first describe steps for optimization of genotyping primers, followed by detailed guidance on the preparation of both scATAC-seq and single-cell genotyping libraries, fully automated on high-throughput liquid handling platforms.
For complete details on the use and execution of this protocol, please refer to Turkalj, Jakobsen et al.¹

Authors: Turkalj, S; Jakobsen, NA; Groom, A; Radtke, FA; Vyas, P

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Cell Press
• Journal: STAR Protocols
• Volume: 4
• Issue: 4
• Article number: 102641
• Place of publication: United States
• Publication date: 2023-10-26
• Acceptance date: 2023-09-22
• DOI: 10.1016/j.xpro.2023.102641
• EISSN: 2666-1667
• Pmid: 37897733
• Language: English
• Keywords: bioinformatics; genetics; cancer; genomics; single cell; molecular biology; sequence analysis; sequencing; stem cells