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

ABSTRACT: 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.

SUBMITTER: Turkalj S

PROVIDER: S-EPMC10641301 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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

Turkalj Sven S Jakobsen Niels Asger NA Groom Angus A Radtke Felix A FA Vyas Paresh P

STAR protocols 20231026 4

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, fo ...[more]

PMID: 37897733

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