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. 2023 Nov 30;55(12):2104–2116. doi: 10.1038/s41588-023-01572-y

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© The Author(s) 2023

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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Extended Data Fig. 6 — a. Overview of analytical steps (left) and density plot showing the distribution of Pearson correlation coefficients between gene expression and the accessibility of distal linked site (colored in red) or all nearby accessible elements (within ±500 kb of the promoter, colored in gray) across pseudo-cells. Dash line indicates the Pearson correlation coefficient cutoff with 0.01 FDR. b. Left, histogram showing the number of accessible sites per gene. Right, histogram shows the distance distribution of accessible sites within 500 kb of genes. Both plots include all nearby accessible sites (colored in black) and the linked accessible sites (colored in red). c. Heatmaps showing the concordant expression of genes (left) and accessibility of putative distal linked sites (right) across all matched subclusters. Rows represent the aggregated gene expression or peak accessibility for a given subcluster. The raw aggregated RNA-seq and ATAC-seq data was normalized first by the total number of reads for each subcluster and then scaled to Z-score across all subtypes. d. Correlation plot showing examples of subcluster-specific genes and linked accessible sites for microglia-9 and unipolar brush cells-2. Gray area indicates 95% confidence intervals around the linear regression line.