Extended Data Fig. 4: Characterization of epigenomic changes in patient samples.
a, Differential peaks from the H3K27me3 (left) and H3K27ac (right) CUT&Tag data. The fold change and two-tailed Wald test P values were calculated by DESeq2. The H3K27me3 (left) volcano plot shows increased peaks (P < 0.05 and log2(fold change) > 0.5, n = 77) and decreased peaks (P < 0.05 and log2(fold change) < −0.5, n = 502) in red and blue, respectively. The H3K27ac (right) volcano plot shows increased peaks (P < 0.05 and log2(fold change) > 0.5, n = 816) and decreased peaks (P < 0.05 and log2(fold change) < −0.5, n = 2,844) in red and blue, respectively. b, Differential chromatin accessibility between patient and control samples in nine cell types from the snATAC-seq. Increased peaks (one-tailed Poisson test Padj < 0.01, log2(fold change) > 0.585 and RPKM > 1 in Cov) and decreased peaks (one-tailed Poisson test Padj < 0.01, log2(fold change) < −0.585 and RPKM > 1 in Ctrl) are shown in red and blue, respectively. c,d, HOMER motif analysis of both increased (top) and decreased (bottom) peaks from the bulk ATAC-seq (c) and the H3K27ac CUT&Tag (d). P values were calculated using a one-tailed hypergeometric test. e, Genome browser screenshot (left) and violin plot (right) showing the upregulation of the NCOA1 gene in syncytiotrophoblasts (ST). The pseudo-bulk tracks of ST cells from the snRNA-seq are displayed as RPM and the y axes range from 0 to 5 (left). The y axis of the violin plot shows the expression of NCOA1 in ST cells from the snRNA-seq calculated by Seurat (right).
