Extended Data Fig. 7: Bulk RNAseq analysis of T cells isolated from brains of Mg^ΔIfnγr mice and littermate controls.

(a) Sorting strategy for isolation of CD25^hi (Treg) and CD25⁻ (Teff) cells from brains of Mg^ΔIfnγr mice and littermate controls. (b) Normalized reads of selected genes from sorted CD25⁻ (Teff) and CD25^hi (Treg) cells extracted from B6/SJL Mg^ΔIfnγr and control mice at REM stage of RR-EAE, representing Treg genes not changed between Mg^ΔIfnγr and control. n = 6 individual mice per group, lines represent mean. (c) Normalized reads of selected genes from sorted CD25^- (Teff) and CD25^hi (Treg) cells extracted from B6/SJL Mg^ΔIfnγr and control mice at REM stage of RR-EAE, representing genes significantly changed in Treg cells between Mg^ΔIfnγr and control. n = 6 individual mice per group, lines represent mean. (d) GSEA comparison WT and Mg^ΔIfnγr T reg cell transcriptomes with list of genes upregulated in WT CNS Treg cells vs. splenic Treg cells⁶. Normalized enrichment score (NES) and the false discovery rate (FDR) are shown in the enrichment plot. Normalized enrichment score = −1.04, FDR q-value = 0.34. This indicates that Treg cells from Mg^ΔIfnγr brains do not acquire features of a CNS Treg signature.