Spatially-mapped single-cell chromatin accessibility

High-throughput single-cell genomic assays resolve the heterogeneity of cell states in complex tissues; however, the spatial orientation within the network of interconnected cells is lost. As cell localization is a necessary dimension in understanding complex tissues and disease states, we present a novel method for highly-scalable spatially-resolved single-cell profiling of chromatin states. We use high density multiregional sampling to perform single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin (sciMAP-ATAC) to produce single-cell data of equivalent quality to non-spatial single-cell ATAC-seq. We apply sciMAP-ATAC in the adult mouse cortex to discriminate cortical layering of glutamatergic neurons and establish the spatial ordering of single cells within intact tissue. We then leverage this spatially-oriented cell dataset by combining it with non-spatially resolved whole brain sci-ATAC-seq data and assess layer-specific marker gene chromatin accessibility and transcription factor motif enrichment. Using sciMAP-ATAC seq, we identify sets of regulatory elements that spatially vary in the cortex, which includes canonical layer-specific markers and previously unannotated putative regulatory elements.