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. 2021 Feb 24;12:1274. doi: 10.1038/s41467-021-21515-7

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a Experiment schematic of sciMAP-ATAC in the mouse somatosensory cortex. b DAPI and SATB2 staining of SSp cortex from sciMAP-ATAC histological section (scale bar, 50 µm) in reference to matched rerference atlas image (Allen Mouse Brain Atlas: http://atlas.brain-map.org/atlas?atlas=1&plate=100960312, ref. ²⁵). c UMAP of 7779 cells colored by punch location category. Each category contains cells from 32 spatially distinct tissue punches. d UMAP as in c, colored by cell type (OPC oligodendrocyte precursor cells, Int Olig intermediate oligodendrocytes, Mat Olig mature oligodendrocytes, Astro astrocytes, Endo endothelia, Micro microglia, MSN medium spiny neurons, GABA GABAergic (inhibitory) neurons, Glut glutamatergic (excitatory) neurons). e ATAC-seq profiles for cells aggregated by cell type for marker genes; colored by cell type as in d. f Aggregate cell type composition over punches belonging to the broad region categories; colored by cell type as in d. g Cell type composition for each of the 96 individual punches split by broad region category; colored by cell type as in d. Source data are provided as a Source data file.