Transcriptomic profiling of EAE astrocytes and microglia +/- B cell depletion

ACSA-2+ astrocytes or CD11b+ microglia/macrophages were isolated from the EAE (MOG 1-125) spinal cord 3 days after animals reached a clinical score of 2.5 when animals were given either anti-CD19/anti-B220 or control antibody. Each treatment group consists of 3-4 RNA samples. Sequencing was performed using TruSeq Stranded Total Gold. Batch effect mitigation was done to remediate batch effects across two sequencing batches. Limma-voom was utilized for differential expression analysis. Each file contains Gene ID, estimated log2 fold change (logFC), average log2 expression (AveExpr), test statistic (t), raw P-value (P.value), FDR adjusted P-value (adj.P.value), and B-statistic (B). "Comparison 1" file is B cell depleted EAE astrocytes vs control EAE astrocytes. "Comparison 2" file is B cell depleted EAE astrocytes vs healthy control astrocytes. "Comparison 3" file is control EAE astrocytes vs healthy control astrocytes. "Comparison 4" file is B cell depleted EAE microglia vs control EAE microglia. "Comparison 5" file is B cell depleted EAE microglia vs healthy control microglia. "Comparison 6" file is control EAE microglia vs healthy control microglia. "BatchEff_PCA" file has PCA plots of the two sequencing batches showing Cell Type 1 (astrocytes) and Cell Type 2 (microglia).