We implemented in silico estimation of the relative proportions of five cell types (ESCs, ES-derived NPCs, and derived dopamine neurons from culture53, and adult cortex neuronal and non-neuronal cells from adult tissue54) using epigenome-wide DNAm data using a recently published algorithm55. All data was obtained using the Illumina HumanMethylation450 (“450k”) microarray platform from GEO56. After normalizing the publicly available data together using the preprocessQuantile function in the minfi Bioconductor package20, we picked the cell type-discriminating probes as outlined by Jaffe and Irizarry57 resulting in 405 unique probes that distinguished the five cell types. Projecting the brain samples onto these profiles results in a composition proportion for each cell type and sample (see Figure 2). We computed the percentage of variance explained (R2), comparing a linear model with all five composition profiles to an intercept-only model at each Illumina 450k probe and gene expression probe.
