Fig. 3
oMG microglia gene expression profile is highly comparable to microglia(-like) cells. a Unsupervised hierarchical cluster analysis on DESeq2 rlog transformed raw counts of oMG day 38, oMG day 52, adult MG1, iPSC, and fibroblasts based on all genes after removal of common genes (FDR > 0.05, sum of raw read counts > 0) between samples. b Spearman correlation matrix for the correlations between oMG day 38, oMG day 52, adult MG1, iPSC and fibroblast DESeq2 rlog transformed raw counts of genes used in Fig. 3a. Median rlog gene counts of the biological replicates were used as input. The size and color of circles show the strength and direction of the correlation, respectively. c Heatplot representation of DESeq2 normalized expression levels for several microglia markers23, 24, 34 in iPSCs fibroblasts, oMG day 38, oMG day 52, and adult MG1. d Plotted DESeq2 normalized expression of a selection of microglia typical genes in oMG at day 52 and adult MG1. e Temporal mRNA expression of characteristic microglia markers. Microglia were enriched with CD11b-MACs from organoids after 52 or 119 days in culture. mRNA levels were assessed by qRT-PCR and normalized to the geomean of the reference genes SDHA2 and ACTB. Data points represent mRNA levels of oMG 1, 3, and 5. f Unsupervised hierarchical cluster analysis on log transformed FPKM values for all available gene expression data of oMG day 38 and 52, adult MG1, fetal MG, another iPSC-derived microglia model (iPSC MG; GSE85839)24 and additional primary adult microglia (adult MG2; GSE73721)25. Prior to hierarchical clustering, log transformed FPKM values were scaled for each sample. See also Supplementary Fig. 4, and Supplementary Data 1 and 2
