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Fig. 2 | Epigenetics & Chromatin

Fig. 2

From: Epigenetic dynamics of monocyte-to-macrophage differentiation

Fig. 2

DNA methylation analysis. a PCA on whole-genome bisulfite data. A clear separation of monocytes (Mo) and macrophages (Mac) as well as donors Hm03 and Hm05 is visible. b Representative example of a DMR in the left part of an IGV browser snapshot. The DMR coincides with the gain of a NOMe peak. c Comparison of the average methylated DNA fraction in the identified DMRs in a variety of tissues subjected to WGBS [12]. Boxplots showing medians, 75th and 25th percentile (box limits) and whiskers of 1.5 × IQR, p < 0.0001 (unpaired Student’s t test) for Mac against all other tissues. d Validation of 10 DMRs by targeted deep bisulfite sequencing. Average CpG methylated fractions in monocytes and macrophages after at least 3 days of differentiation. Results are mean ± SD from 4 independent donor samples (Hm03, Hm04, Hm05 and Hm06). **p value <0.01; ***p value <0.001 (two-tailed paired Student’s t test). Related to Additional file 6: Figure S3. e Representative comparative methylation plot (DMR33). Samples are sorted by overall methylation. Related to Additional file 6: Figure S3. f Distribution plot of expression changes for all genes (yellow), genes within the same TAD (blue) and genes identified in the GREAT analysis (green)

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