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. Author manuscript; available in PMC: 2016 Jun 19.
Published in final edited form as: Circ Res. 2015 Apr 22;117(1):17–28. doi: 10.1161/CIRCRESAHA.117.305860

Figure 4. RNA-Seq transcriptome analysis of iPSC, IPSDM and HMDM.

Figure 4

(A) Schematic figure of RNA-Seq design and data analysis (n=3 subjects, Control-1, Control-3 and Control-4, with two iPSC clones per subject). (B) Multidimensional scaling (MDS) and (C) co-regulation analysis (CRA) confirmed the distinct transcriptome profile of iPSC from HMDM and IPSDM. M1 polarization profoundly affects the transcriptional profile while M2 polarization results in more subtle expression changes. (D) IPSDM showed expression of macrophage markers and the absence of markers of pluripotency and other hepatopoietic cells. (E) and (F) show the total number of genes (FPKM > 1% expression of all genes) and DE genes in iPSC vs. IPSDM, and IPSDM vs. HMDM. The top 10 gene ontology (GO) terms ranked by FDR-adjusted P values for DE genes are illustrated. The size of the circle is inversely correlated to FDR-adjusted P values of enrichment in the respective GO term. The thickness of the lines corresponds to similarity between two GO terms. Scatterplot (F) suggests the strong Pearson’s correlation (r=0.85) of transcriptome between HMDM and IPSDM. Green, DE genes with higher expression in M0-HMDM; Red, DE genes with higher expression in M0-IPSDM; Blue, non-DE genes.