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. 2022 Mar 3;54(3):306–317. doi: 10.1038/s41588-022-01014-1

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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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Extended Data Fig. 8 — (A-C) Quality control for Smart-seq2 libraries from CASTxC57 primary fibroblast cells. Red lines represent quality control cutoff. (A) Boxplot showing number of sequenced reads counts mapped to exons (Smart-seq2 libraries, n = 218 cells). The center line shows the median, interquartile limits indicate the 25^th and 75^th percentiles and whiskers denote the farthest points at a maximum of 1.5 times the IQR. (B) Scatter plot showing the distribution of allele sensitive read counts for non-imprinted autosomal genes. (C) Scatter plot showing the distribution of allele sensitive read counts for non-escapee genes on the X-chromosome. (D) Scatter plot of the allelic imbalance against p-values (binomial test, Benjamini-Hochberg adjusted) across fibroblasts (n = 751 cells). (E) Density plot summarizing observed allelic imbalance of lncRNAs and mRNAs across fibroblasts (n = 751 cells). (F) Mean expression towards the median of allelic imbalance of a sliding window (width = 25) for mRNAs and lncRNAs. The green and blue lines denote a loess fit to the sliding window with a 95% confidence interval for mRNAs and lncRNAs, respectively. (G) Schematics from the UCSC genome browser representing the gene loci of four candidate lncRNA-mRNA gene pair interactions. (H) Scatter plot representing allelic imbalance of genes within + /−500kb (of lncRNA TSS) of candidate genes. Candidate lncRNA-mRNA gene pair interactions are colored in red.