Figure 4

Comparison of T-DMRs from high- and low-input samples identified using MeKL-chip. (A) Correlation of differential methylation between retina and brain (ΔM) from high- and low-input arrays at T-DMRs initially identified within the 250-ng samples. (B) Relationship between ΔM of T-DMRs for high-input and that of randomly shuffled probes for the 10, 25 and 50 ng low-input arrays. (C) Distribution of CpGO/E (top panel) and CpG density (bottom panel) of verified T-DMRs for all three low-input arrays, dropouts from only one low-input array, and dropouts from at least two low-input arrays. (D) Percentage of T-DMRs and dropouts from at least two low-input arrays that were associated with retina-/brain-enriched genes identified from previously published exon array data. c.c: correlation coefficient; CpGO/E: observed-to-expected CpG ratio; MeKL: MBD2b/MBD3L1 enrichment of DNA followed by KLM-PCR; T-DMR: tissue-specific differentially methylated region.