High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell KO]

Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels. Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. ASAP-seq makes use of a novel bridging approach to utilize existing commercially available antibody:oligo conjugates developed for CITE-seq and related technologies. We demonstrate the utility of ASAP-seq in the context of hematopoietic differentiation, cell surface marker dynamics following peripheral blood mononuclear cell stimulation, and as a combinatorial decoder of multiplexed perturbations in primary T cells. Overall design: Sorted human T-cells from 3 biological donors were activated and target genes were perturbed using CRISPR / Cas9. Gene KOs were generated in a pooled fashion using gRNAs targeting CD4 (HTO2), ZAP70 (HTO4), NFKB2 (HTO5), CD3E (HTO3 + HTO13), CD3E+CD4 (HTO3 + HTO12) and 2 non-targeting controls (NTCs; HTO1). Different gRNA replicates were encoded using HTO12 and HTO13 for CD4, ZAP70, NFKB2, and NTC conditions. Changes in chromatin accessibility and protein abundance were determined concomitantly in single cells.