Effect of PPAR-delta on murine microglia gene expression during experimental autoimmune encephalomyelitis

Mice were generated that had a tamoxifen-inducible Cre recombinase transgene under the control of the CX3CR1 promoter. These mice were crossed with mice that had a floxed PPAR-delta allele. EAE was induced in these mice and controls that just had the floxed allele at 30 days after tamoxifen treatment. Mice were euthanized (N=9/genotype) for isolation of microglia at 2-3 days after the onset of EAE, a time when clinical scores were equivalent between the groups. Spinal cords were pooled (N=3/sample) for microglia isolation and sorting. Microglia were isolated from spinal cords by collagenase digestion, percoll gradient and FACS sorting using CD45 and CD11b antibodies resulting in N=3 spinal cords resulting in N=3 pooled samples/group. RNA was isolated from sorted microglia using the PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific). RNA quality was evaluated using the 2100 Bioanalyzer (Agilent) and N=2 samples per group with RIN numbers > 7 were submitted for sequencing and analysis at the UHN Bioinformatics and HPC Core, Princess Margaret Cancer Centre. Two samples are microglia from CX3CR1-CreERT PPARdelta floxed mice and two samples are from PPARdelta floxed mice. All mice had EAE for 2-3 days at the time of microglia isolation.