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. 2021 Oct 6;598(7879):103–110. doi: 10.1038/s41586-021-03500-8

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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. 3 — a, b, Regulatory regions were identified in each cell type using DMRs (n = 1,302,403) (a) and open chromatin regions (ATAC peaks; n = 316,788) (b) in multimodal integrated clusters. c, d, Saturation analysis for two excitatory subclasses shows the number of regulatory regions detected as a function of sampled cells. e, Saturation analysis of the number of transcription factor DNA-binding sequence motifs enriched in DMRs of each cell type. f, Enrichment of motifs for selected transcription factor families as a function of the number of cells sampled. g, Browser views of loci containing cell-type-specific regulatory elements (grey highlighted regions). The Rfx3 gene is differentially expressed in L2/3 neurons and has an enhancer specific to L2/3 located approximately 15 kb upstream of the promoter region. h, i, Examples of intergenic regions with accessibility and demethylation specific to L6 CT (h) or L2/3 (i) neurons. The black bars indicate predicted regulatory regions.