Fig. 3

Deconvolution of in vitro mixed PBMC and intestinal organoid DNA based on HOXA3 DNA methylation. a The ratio of Intestinal organoid to PBMC DNA used in the in vitro mixes. b Example methylation heatmap outputs of the HOXA3 amplicon for PBMCs (left), 50:50 mix (centre), and intestinal organoid (right). Each row represents an individual read, and each column is a CpG site within the amplicon; column names refer to the CpG position in the read. c Density plot for the number of methylated CpG sites per read in pure intestinal organoid (blue) and pure PBMC (red) samples. The y-axis represents the probability per unit on the x-axis such that the area under the curve for a specific interval is equal to the probability of the number of methylated CpGs in that interval. Bandwidth is 0.45. d Stacked bar chart of the proportion of classified for each sample type. Reads were classified as intestinal organoid (blue), PBMC (red), or unclassified (grey). e Scatter plot of observed read classification vs expected read classification for intestinal organoid and PBMC