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. 2022 Nov 24;41(6):832–844. doi: 10.1038/s41587-022-01551-4

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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. 5 — (a, b) Haplotype-specific NO analysis of NO at gene bodies genome-wide in RPE-1 (a) and BM510 (b). For each chromosomal karyogram, the y-axis indicates the significance of haplotype-specific NO for each gene (-log10 p.adjust). All the significant genes were indicated in red dots (FDR 10%; two-sided wilcoxon rank sum test followed by Benjamini Hochberg multiple correction; derived from n = 33 cells and n = 79 cells for RPE-1 and BM510, respectively; Boxplots were defined by minima = 25th percentile - 1.5X interquartile range (IQR), maxima = 75th percentile + 1.5X IQR, center = median, and bounds of box = 25th and 75th percentile.). NTRK3 (identified in BM510) is the only significant gene adjacent to an SV breakpoint. Haplotype-resolved RNA expression at the NTRK3 locus is depicted using bar graphs in the right panel (two-sided likelihood ratio test followed by Benjamini Hochberg multiple correction; n = 2 biological replicates; Data are presented as mean values +/− SEM). (c-d) Haplotype-specific NO analysis at CREs. Browser track depicts the haplotype-resolved NO of the not rearranged (Ref) homolog in red, and the SV homolog in blue. scNOVA identified two CREs with significant haplotype-specific NO, including an intergenic CRE spanning chr15:87527100-87528100 (p.adjust = 0.029, log2-fold change = −2.01) (c) and an intronic CRE at chr15:88246388-88247388 (p.adjust = 0.076, log2-fold change = −1.39) (d).