Transcriptome analysis of Tregs (CD4+Foxp3+) and Tcons (CD4+Foxp3-) from spleen and CNS of naïve mice and at the peak of EAE

Tregs and Tcons were isolated by flow cytometry from the spleen of naïve mice and from the spleen and central nervous system (brain + spinal cord) (CNS) of mice at the peak of experimental autoimmune encephalomyelitis (EAE) induced by immunization with MOG(35-55). Samples at EAE peak were collected at day 16-18 after immunization. Purity was >99.5%. Foxp3.eGFP mice (provided by A. Rudensky) were used to identify Tregs. A bin channel excluded CD11b+ cells during the sort. Mice were 6-10 weeks of age at the time of immunization. The goal was to identify genes differentially expressed between Tregs and Tcons from naive mice, and genes differentially expressed by these cells in the inflamed tissue (central nervous system) at the peak of the disease. The experiments include a total of 20 arrays, each corresponding to a distinct biological sample. There are 3 arrays (3 samples) for Tregs from the spleen of naïve mice, and 3 arrays (3 samples) for Tconvs from the spleen of naïve mice. There are 4 arrays (4 samples) for Tregs from the spleen of EAE mice, and 3 arrays (3 samples) for Tconvs from the spleen of EAE mice. There are 3 arrays (3 samples) for Tregs from the CNS of EAE mice, and 4 arrays (4 samples) for Tconvs from the CNS of EAE mice.