Supplementary Figure 8: Transcriptional profiling of purified SC microglia.

(a) SC homogenate from rNLS8 and nTg littermates were subjected to FACS analysis and DRAQ5/CD45/CD11b+ microglia purification for RNA-seq. Shown here is the gating strategy and purity of sorted microglia. (b) Total RNA extracted from the following sorted samples: controls (green, pooled rNLS8 on DOX and nTg, n = 14); early disease (purple, rNLS8 2 weeks off DOX, n = 8); late disease (red, rNLS8 6 weeks off DOX, n = 7), and recovery (blue, rNLS8 6 weeks off + 1 week on DOX, n = 9). Bars represent mean ± S.D. (c) PCA of SC samples (n = 38) described in (b) shows some clustering of disease groups, though early and late disease groups are less discrete. (d) Cell lineage specific gene expression shows that all groups have high expression of microglial genes (Cx3cr1, Irf8), but low/absent markers for astrocytes (Gfap) and neurons (Nefh). Whiskers in box plots show minima and maxima, and box shows Q1-Q3 with median indicated, with individual points represented by squares overlaid. Group sizes are same as in (b). (e) Hierarchical clustering of all samples from SC based on logarithm of expression > 10 (7771 genes), shows some overlap between disease samples at different time-points. Yellow and blue indicate higher and lower expression levels, respectively.