Abstract
High-throughput single-cell epigenomic assays can resolve cell type heterogeneity in complex tissues, however, spatial orientation is lost. Here, we present single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin, or sciMAP-ATAC, as a method for highly scalable, spatially resolved, single-cell profiling of chromatin states. sciMAP-ATAC produces data of equivalent quality to non-spatial sci-ATAC and retains the positional information of each cell within a 214 micron cubic region, with up to hundreds of tracked positions in a single experiment. We apply sciMAP-ATAC to assess cortical lamination in the adult mouse primary somatosensory cortex and in the human primary visual cortex, where we produce spatial trajectories and integrate our data with non-spatial single-nucleus RNA and other chromatin accessibility single-cell datasets. Finally, we characterize the spatially progressive nature of cerebral ischemic infarction in the mouse brain using a model of transient middle cerebral artery occlusion.
Highlights
High-throughput single-cell epigenomic assays can resolve cell type heterogeneity in complex tissues, spatial orientation is lost
We and others have explored methods for tissue preservation that are compatible with singlecell ATAC-seq[18,22]; we sought to confirm that these strategies are compatible with freezing techniques used for cryosectioning and IHC staining of tissue
We tested our workflow on mouse whole brain samples by processing one hemisphere using flash-freezing methods designed for tissue freezing medium (TFM) embedding and cryosectioning (“methods of punch dissociation (Methods)”), and processing the paired hemisphere as fresh tissue
Summary
High-throughput single-cell epigenomic assays can resolve cell type heterogeneity in complex tissues, spatial orientation is lost. Layer-specific gene expression profiles of cortical neurons and astrocytes have been characterized by spatial transcriptomic approaches and immunohistochemical (IHC) staining; spatially mapped epigenetic states of cortical cells have yet to be directly assayed, without relying on the data integration[5,6,7] To address this challenge, several strategies have emerged to assay transcription either directly in situ or in a regional manner. Technologies that utilize array-based mRNA barcoding do not require a defined set of genes and operate to single-cell RNA-seq methods[13,14], allowing for whole transcriptome profiling Initial iterations of these platforms capture regional transcription over multiple cells; higher resolution variants may facilitate single-cell resolution. We demonstrate the utility of sciMAP-ATAC by profiling the murine and human cortex, where distinct cell type compositions and chromatin profiles are observed based on the spatial orientation of the punches, and further extend the platform to characterize cerebral ischemic injury in a mouse model system, where cell type compositions and epigenetic states are metered by proximity to the injury site (Supplementary Fig. 1)
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