Extended Data Fig. 5: Epigenetic landscape recovery.
a, Western blot showing H3K27 acetylation in DMSO, TSA and the indicated time intervals following TSA washout. Lamin B1 is shown as loading control. b, Cell generation tracing using flow cytometry following DMSO and TSA treatment. Two biological replicates are shown. c, ChIP–qPCR showing H3K27ac signal in DMSO, TSA and 24-h recovery (REC) conditions at the ActB and Oct4 promoters that have high levels of acetylation (left) and at the Zfp608 promoter and an Oct4 upstream region largely devoid of acetylation (right). Bar charts are mean of two biological replicates ±s.e.m., scatterplot shows individual replicates. d, Spike-in normalized H3K27ac ChIP–seq signal per chromosome (n = 19) in replicate 3. Data shown are the median, with hinges corresponding to IQR and whiskers extending to the lowest and highest values within 1.5× IQR. e, Heatmaps showing scaled ChIP–seq signal per epitope in merged replicates at all enrichment sites in DMSO, TSA and REC conditions. f, Western blots showing total level of histone modifications in nuclear extracts. Lamin B is shown as loading control. g, Diverging bar chart showing the number of differential ChIP–seq and ATAC–seq peaks identified by DESeq2 analysis in TSA versus DMSO (TSA) and 24-h recovery versus DMSO (REC) conditions. h, Western blot showing TSA-induced H3K9 hyperacetylation and recovery in nuclear extracts. Lamin B1 is shown as loading control. i, Diverging bar chart showing the number of differential H3K9ac ChIP–seq peaks identified by DESeq2 analysis. j, Heatmaps showing scaled H3K9ac ChIP–seq signal in merged replicates at all enrichment sites in DMSO, TSA and REC conditions. Box plots (elements as in d) of normalized ChIP–seq signal at all H3K9ac sites (n = 60618) are shown above heatmaps.
