Additional file 2: Figures S1-S3. of Placental methylome analysis from a prospective autism study

Figure 1. Histograms of average methylation in 20 kb windows for each placental sample. Individual histograms (no smoothing) for each MARBLES typical and autism placentas as well as three biological replicates of “normal” non-MARBLES placentas which have no known pathologies [16]. Methylation data was omitted if a window had fewer than 20 covered CpG sites. Red vertical lines show the arbitrary 60% methylation cutoff between windows with low and high methylation. Percentage of 20 kb windows with average methylation below 60% also shown in red (excluding omitted windows). n = number of windows with required CpG coverage, m = number of windows omitted due to insufficient coverage. Figure S2. Plots showing location and statistical significance of differential methylation in HMDs and PMDs. Each point shows the FDR-corrected probability of that HMD/PMD being differentially methylated between autism and typical MARBLES placentas. Chromosomes are alternately colored red and black for clarity. The blue line shows the 0.05 cutoff for statistical significance. Figure S3. DLL1 Pyrosequencing results by individual CpG position. Three CpG sites corresponding to the H3K27ac/H3K4me1 peaks were assayed by pyrosequencing on the same samples analyzed by MethylC-seq (region shown by gray bar in Fig. 4a within circled HMD). (PDF 3999 kb)