Spatially mapped single-cell chromatin accessibility.

IF: 17.694

Cited by: 43

Datasets

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.

Keywords

Spatial Transcriptomics

sciMAP-ATAC

MeSH terms

Animals

Brain

Brain Ischemia

Cell Nucleus

Chromatin

Female

Immunohistochemistry

Infarction, Middle Cerebral Artery

Mice

Authors

Thornton, Casey A

Mulqueen, Ryan M

Torkenczy, Kristof A

Nishida, Andrew

Lowenstein, Eve G

Fields, Andrew J

Steemers, Frank J

Zhang, Wenri

McConnell, Heather L

Woltjer, Randy L

Mishra, Anusha

Wright, Kevin M

Adey, Andrew C

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