Figure 4
ScTrio-seq analyses of single HCC cells. (A) Global DNA methylation levels of CpG sites of HepG2 cells and HCC cells. Each circle represents the DNA methylation of one single cell, and the lines represent the bulk or average (single-cell) results. HCC bulk (for the regions also detected in scRRBS) represents the DNA methylation of HCC-bulk cells, the calculation for which only includes regions that are also detected in the HCC scTrio-seq data. (B) Average CpG methylation levels in gene bodies (from TSSs to TESs) of all RefSeq genes and their 15-kb flanking regions in HepG2 cells and HCC cells. (C) Heat map showing normalized copy-number values of 10-Mb windows deduced from RRBS data of scTrio-seq analysis. The HCC cells are clustered based on their CNV patterns. (D) Heat map showing relative gene expression levels in each 10-Mb genomic window. The HCC cells are clustered based on their expression levels in each genomic window. (E) The concordance of the DNA methylation of normal liver cells and that of HCC cells. Each dot shows the Pearson correlation coefficient between any two single cells within each group.
