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

• Published in: STAR protocols 2023-12, Vol.4 (4), p.102641-102641, Article 102641
• Main Authors: Turkalj, Sven, Jakobsen, Niels Asger, Groom, Angus, Radtke, Felix A., Vyas, Paresh
• Format: Article
• Language: English
• Subjects: Bioinformatics; Biological Assay; Cancer; Chromatin - genetics; DNA Primers; Epigenomics; Genetics; Genomics; Genotype; Molecular Biology; Protocol; Sequence Analysis; Sequencing; Single Cell; Stem Cells
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2023.102641

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 [Display omitted] •scATAC-seq coupled with high-sensitivity mutation capture at multiple genomic loci•Link genetic and epigenetic evolution in malignant and pre-malignant tissues•Guidance on barcoding, automation, and liquid handling for high-throughput applications Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.