Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq

Multi-modal profiling of different molecular layers from the same single cell enables more comprehensive characterisations of cellular heterogeneity compared to conventional single-modality approaches. A key example is co-detection of chromatin accessibility and gene expression that offers the opportunity to investigate the cell type-resolved gene regulatory mechanisms. Here, we described a sensitive and robust protocol of in situ SHERRY after ATAC-seq (ISSAAC-seq) for the concurrent measurement of chromatin accessibility and gene expression from the same single nucleus. The method begins with dual Tn5 tagging of open chromatin regions and DNA/RNA hybrid after reverse transcription that take place in bulk nuclei. Then various single-nucleus isolation strategies can be used based on the experimental purpose of the user. The protocol is highly modular with flexible throughputs ranging from several hundreds to tens of thousands of nuclei. The generated data are of high quality in both modalities. The entire workflow can be finished within 1 or 2 days, and the procedures works on multiple different platforms.