Figure 3 | Scientific Reports

Figure 3

From: Transcriptomics uncovers substantial variability associated with alterations in manufacturing processes of macrophage cell therapy products

Figure 3

M1/M2a marker genes’ expression. (a) Volcano plot of differential gene expression for M2a_vs_M1 comparison between M1 and M2a macrophages, with classical M1 and M2a marker genes indicated. (b) Venn diagram analysis to identify genes with highest expression in M2a. Overlap of at least 16-fold upregulated genes (LFC4: log2foldchange > 4, s < 0.0001 and base mean > 40) in M2a_vs_M0 and M2a_vs_M1 comparison defines our M2a marker genes (15) with (c) their expression visualized in a heatmap; (d) Venn diagram analysis to identify genes with highest expression in M1. Overlap of at least 16-fold upregulated genes (LFC4: log2foldchange > 4, s < 0.0001 and base mean > 40) in M1_vs_M0 and M1_vs_M2a comparison defines our M1 marker genes (224). (e) Network analysis using STRING of the gene set overlap identified in (d) excluding literature gene set. In red are genes assigned to GO:000695 ~ ”immune response”, in green—GO:0032496 ~ “response to LPS” and in blue—GO:0002376 ~ “immune system process”.

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