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.对未分化胚胎干细胞（Embryonic Stem Cells, ESCs）以及分化第4天和第16天的对应拟胚体（Embryoid Bodies, EBs）的RNA样本开展基因芯片表达谱分析。A) 针对各细胞系、各时间点的独立生物学重复样本进行二维主成分分析。B) 相较于野生型（wild type, wt）胚胎干细胞，展示Dnmt1−/−（蓝色圆圈）与三重敲除（TKO，绿色圆圈）胚胎干细胞中差异表达基因的韦恩图。(C、D) 展示敲除型与野生型（红色圆圈）拟胚体在分化第0-4天（C）及第4-16天（D）阶段的基因表达变化韦恩图。本研究对野生型与突变型拟胚体在两个分化区间内的基因表达变化进行鉴定与比较：较大数字代表总基因变化数，较小数字分别对应各分区中上调（↑）与下调（↓）的基因数量。所有数据均取自独立生物学重复的平均值。