TY - JOUR
T1 - Spatially mapped single-cell chromatin accessibility
AU - Thornton, Casey A.
AU - Mulqueen, Ryan M.
AU - Torkenczy, Kristof A.
AU - Nishida, Andrew
AU - Lowenstein, Eve G.
AU - Fields, Andrew J.
AU - Steemers, Frank J.
AU - Zhang, Wenri
AU - McConnell, Heather L.
AU - Woltjer, Randy L.
AU - Mishra, Anusha
AU - Wright, Kevin M.
AU - Adey, Andrew C.
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/1
Y1 - 2021/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85101584248&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85101584248&partnerID=8YFLogxK
U2 - 10.1038/s41467-021-21515-7
DO - 10.1038/s41467-021-21515-7
M3 - Article
C2 - 33627658
AN - SCOPUS:85101584248
SN - 2041-1723
VL - 12
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 1274
ER -