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. 2022 Dec 9;13:7627. doi: 10.1038/s41467-022-35374-3

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© The Author(s) 2022

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. 4 — a UMAP projection of the three sciMETv2 preparations integrated together colored by cluster. b Global CH methylation levels per cell in the UMAP projection (left) and by cluster (right). For all boxplots, boxes indicate median, 25th and 75th percentiles with min and max lines as 1.5x interquartile range. c Promoter CG methylation levels of marker genes for cell-type-aggregated clusters (left) and both promoter CG methylation and gene body CH methylation for neuronal marker genes and subtype markers. Dashed lines represent clusters showing evidence of positive gene regulation for excitatory (top) or inhibitory (bottom) marker genes.