Genome-wide expression analysis of wt, Dnmt1−/− and TKO ESCs during differentiation as EBs.

RNA samples from undifferentiated ESCs and respective EBs at day 4 and 16 of differentiation were subjected to microarray expression analysis. A) Two dimensional principal component analysis of independent biological duplicates per cell line per time point. B) Venn diagram of differentially expressed genes in Dnmt1−/− (blue circles) and TKO (green circles) ESCs with respect to wt ESCs. (C, D) Venn diagram of gene changes occurring between day 0–4 (C) and day 4–16 (D) in knockout and wt (red circles) EBs. Gene changes occurring during the two differentiation intervals in wt and mutant EBs were determined and compared. Larger numbers indicate total numbers of gene changes, whereas smaller numbers refer to up- (↑) and down- (↓) regulated genes in the respective sectors. Data were averaged from independent biological duplicates.