Plate-based ISSAAC-seq for multimodal profiling of chromatin accessibility and gene expression in single cells

Abstract Here, we described a step-by-step protocol for plate-based in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single nucleus. ISSAAC-seq is based on the combination of the recently developed Sequencing HEteRo RNA-DNA-hYbrid (SHERRY) and previously established scATAC-seq approaches, and compatible with both plate-based formats and droplet microfluidics. Plate-based ISSAAC-seq is suitable for small scale preliminary tests at low cost. Main reactions in this protocol are performed in bulk, then single cells were isolated using FACS. Generally, it obtains data quality of ~10,000 ATAC reads in peaks and 2000-5000 detected genes per cell. Library construction for ISSAAC-seq could be completed in 1-2 days. This protocol is related to the publication “ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells” in Nature Methods.