Figure 4

Change in cell state accompanies adaptation of cells to culture. (a) A boxplot showing that 5hmC is enriched in transcribed genes in MEF tissue (blue) and cultured (orange) cells. A gene was classified as expressed if its probes had a combined detection P-value <0.01. ***, P < 0.01, Mann-Whitney U-test. (b) Hierarchical clustering of the principle components of gene expression microarray data upon adaptation of MEF tissue to culture showing that the transcriptome of cultured MEFs is very different from that of the MEF tissue from which they were derived. Tissue samples and culture samples cluster separately. Adaptation to culture also results in a reduction in the sex-specific transcriptional differences between samples. (c) Volcano plot showing the widespread, bi-directional changes in gene expression observed upon adaptation of MEF tissue to culture conditions. Red dots indicate genes losing 5hmC in culture; yellow dots indicate genes gaining 5hmC in culture; blue dots indicate the 100 most outlying genes. The horizontal dashed line indicates P < 0.01; the vertical dashed lines indicate fold change >1.5. (d) Bar chart showing the GO term analysis of genes up-regulated (P < 0.01, fold-change >1.5) for MEFs in culture. The number of individual genes in each category is shown in white. Red line, P = 0.01. (e) Bar chart showing GO term analysis of genes down-regulated (P < 0.01, fold-change >1.5) for MEFs in culture were significantly enriched for epigenetic processes. The number of individual genes in each category is shown in white. Red line, P = 0.01. The x-axis values for (d) and (e) are '-log10(P-value)'.