Extended Data Fig. 6: scPBAT and PBAT-capture of HCT116 clones using a colon cancer oriented probe-set.
From: Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells
a, Distribution of methylation calls in low-depth HCT116 single-cell PBAT analysis. b, Whole genome coverage and on-target coverage for HCT116 clonal populations. Coverage = total number of methylation calls. c, Density plot of pooled average methylation of on-target regions in single cells (black line) and clonal populations (antique-white line). d, Distributions of pooled averaged methylation of on-target regions in clones, grouped by their respective pooled average methylation in single cells (regions with > 50 calls in single cells and > 500 calls in clones, n = 341, 69, 49, 49, 39, 32, 67, 77, 186, 595). e, Pooled average methylation of individual cells in very low (0–1%) and low (1–2%) CG-content regions. f, Trends showing the correspondence between DNA methylation and CpG content for 1,022 single cells. g, Similar to f, showing correlation with genomic replication time. h, Single cell methylation average in regions with low CG-content (0–3%), defining classification into low, mid and high-bg cells i, Distribution of the log2 ratio of coverage of genomic sequences in early- and late-replicating regions. Vertical dashed grey line is defining the threshold for classifying single cells into G1 and S phase. j, Distribution of average methylation per cell in genome-wide low CpG regions (0–3%) for cells inferred to be in G1 and S phases in panel i. nG1 = 254, nS = 767. k, Average promoter and enhancer (methods) methylation in groups of single cells For all groups, n > 6000, chi-squared test, in all cases P < 2*10−16. l, Genomic spatial distribution of colon PBAT-capture probe set. m, Number of regions covered by the probe set, stratified by genomic context. n, Distribution of methylation of covered regions in TCGA colon cancer (COAD). Shown is average methylation of CpGs that reside within (blue) and outside (orange) the PBAT-capture probe set, grouped by genomic context (for all comparisons n > 6000, two-tailed KS test: D > 0.11, P < 2*10−16). o-q, Average methylation of 293 TCGA colon cancer tumors (COAD), in different ranges of CpG content.
