Fig. 4
Minor transcriptional memory in specific HPC/HSC-iPSC lines. a The “4 N-OFF” 20-HPC/HSC-iPSC-18 line is more similar to HPC/HSCs than the “4 N-ON” 20-HPC/HSC-iPSC-16 line; note the similarity of its gene expression profile to that of the HPC/HSC genes with low expression. The green box marks genes that are differentially expressed in the 20-HPC/HSC-iPSC-18 and 20-HPC/HSC-iPSC-16 lines. b The number of highly expressed genes in the 20-HPC/HSC-iPSC-18 line that overlapped with highly expressed genes in the HPC/HSCs was greater than the number that overlapped with genes with low expression in the HPC/HSCs. Sky-blue, HPC/HSC genes with low expression; pink, HPC/HSC genes with high expression; orange, greater than a twofold change between the two cell lines (18 > 16). c The number of highly expressed genes in the 20-HPC/HSC-iPSC-16 line that overlapped with genes with low expression in the HPC/HSCs was greater than the overlap with the HPC/HSC highly expressed genes. The top ten most common enriched GO term categories represented by these genes are plotted. Sky-blue, HPC/HSC genes with low expression; pink, HPC/HSC genes with high expression; pea green, greater than a twofold change between the two cell lines (16 > 18). d Epigenetic modifications in the 332 overlapping genes in the 20-HPC/HSC-iPSC-18 and 20-HPC/HSC-iPSC-16 lines were compared. The distribution of normalized counts for 20-HPC/HSC-iPSC-18 over 20-HPC/HSC-iPSC-16 in the TSS ± 2 kb regions from 332 overlapping genes and from 500 randomly selected genes was plotted (boxplot in R). The horizontal dashed line indicates no difference in the epigenetic modifications between 20-HPC/HSC-iPSC-18 and 20-HPC/HSC-iPSC-16; positive values indicate increased amounts of the modification in 20-HPC/HSC-iPSC-18, and negative values indicate increased amounts of the modification in 20-HPC/HSC-iPSC-16. HPC/HSC hematopoietic progenitor and stem cell, iPSC induced pluripotent stem cell