Extended Data Fig. 1. Focal gain of methylation depends on Dnmt1, is stable, and reproducible.
a, Western blot of DNMT1 (183kDa) in WT, DKO0 and TKOL passage 1, 5 and 10. Loading control: GAPDH (36kDa). n = 1. Violin plot showing average methylation distribution of DMRs (yellow) and CRs (gray) for WT, TKOL P1, TKOL P10, and DKO0 P1. White dots indicate the median; boxes indicate first and third quartiles; whiskers, 1.5 x inter-quartile range; data beyond the end of the whiskers are omitted. b, Genome-wide 1kb window methylation rate distribution of TKOL and DKO0 P15 cells (left). The empirical cumulative distribution curve of the TKOL and DKO0 methylation difference in 1kb windows (right). Dotted line shows the 95% quantile. c, Genomic distribution of DMRs (black lines, n = 2,573). The height of the black line indicates the mean methylation difference of the DMRs (left). DMR and length in base pairs versus CpG count. Methylation difference is indicated by dot color, and the dashed line indicates the coverage adjusted genomic average (right). d, CR (random: light gray, CpG matched: dark gray) length in base pairs versus CpG count. Methylation difference is indicated by dot color and the dashed line indicates the coverage adjusted genomic average. e, Simplified overview of the MeDIP-seq experiment and sample collection. f, Correlation-based clustering of MeDIP-seq replicates for passage 1, 5, and 10 (n = 3 each). The color indicates the correlation value (Spearman correlation). g, Read-counts at DMRs and CRs normalized for the number of regions. Centerline is median; boxes, first and third quartiles; whiskers, 1.5 x inter-quartile range; points are data beyond the end of whiskers. h, Summary plots of aggregated replicates for each of the three passages over DMRs. i, Representative genome browser track showing MeDIP-seq coverage for each replicate (different gray scale).