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. Overall design: 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.