Supplementary Figure 1: Heterogeneity in CP BAMs at the level of IEGs. | Nature Neuroscience

Supplementary Figure 1: Heterogeneity in CP BAMs at the level of IEGs.

From: A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

Supplementary Figure 1

(a) tSNE plot of 3940 cells from the choroid plexus. This shows two main macrophage clusters: CP-BAM A1 and CP-BAM A2, in addition to the smaller macrophage cluster CP-BAM B. (b) Expression of prototypical macrophages genes such as Csf1r, Adgre1 and Fcgr1 confirms that CP-BAM A1, CP-BAM A2 and CP-BAM B are macrophages. (c) Volcano plot showing the genes that are DE between CP-BAM A1 vs. CP-BAM A2 in red. P-value adjustment was performed using bonferroni correction. (d) tSNE plot following regress out of IEGs. This shows that CP BAM-A1 and CP-BAM A2 now cluster as a single population. (e) tSNE maps showing the expression of H2-Aa, Mrc1, Gas6 and Ccr2 before and after IEG regress out. BAM heterogeneity at the level of these genes is more evident after regressing out EGs, showing that IEG induction can overshadow potentially more interesting biological heterogeneity.

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