Analyzing genomic and epigenetic profiles in single cells by hybrid transposase (scGET-seq)

• Published in: STAR protocols Vol. 4; no. 2; p. 102176
• Main Authors: Cittaro, Davide, Lazarević, Dejan, Tonon, Giovanni, Giannese, Francesca
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 16.06.2023; Elsevier
• Subjects: Bioinformatics; Cell Biology; Cell Separation/Fractionation; Genomics; High-throughput Screening; Molecular Biology; Protocol; Sequence Analysis; Sequencing; Single Cell; Molecular Biology; Cell Separation/Fractionation; Genomics; Single Cell; Sequence Analysis; Bioinformatics; Sequencing; High-throughput Screening; Cell Biology
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2023.102176

scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis. For complete details on the use and execution of this protocol, please refer to Tedesco et al. (2022)1 and de Pretis and Cittaro (2022).2 [Display omitted] •Expands standard ATAC-seq approach using hybrid TnH transposase with H3K9me3 tropism•scGET-seq queries accessible and compacted chromatin•scGET-seq allows definition of cell states by analysis of chromatin dynamics Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis.