Gene expression profiling of Th17, Th1*, Treg cells in the spinal cord of EAE mice , and Th17, Treg cells in the SILP of SFB colonized mice

The goal of the RNAseq experiment is to compare gene expression of T cells in different microenvironments. We hypothesized that same T cell subtype (Th17/Th1* cells, or Treg cells in this study) need to change gene expression to adapt to different microenvironments (spinal cord in EAE mice VS. SILP in SFB-colonized mice). By profiling and comparing gene expression of these cells, we were able to identify candidate genes that enable cells for tissue adaptation for functional study. The mice used for T cell isolation were 10-week old IL-17aGfp/+ Foxp3Rfp male littermates (two biological replicates for each sample). Each CD4+ T cell sub-population was sorted with Aria II (EAE Th17: IL-17a+ Klrc1- Foxp3-; EAE Th1*: Klrc1+ Foxp3-; EAE Treg: Foxp3+ IL-17a- Klrc1-; SFB Th17: IL-17a+ Foxp3-; SFB Treg: IL-17a- Foxp3+). EAE samples were isolated at the peak of the disease (Day15, score 5). SFB samples were isolated from stable SFB-colonized mice.