Fatostatin drug treatment of mouse primary microglia cultures

To test the effect of fatostatin on gene expression patterns in microglia, we treated mouse (C57BL/6) primary microglial cultures with fatostatin (5microM, 72h) versus DMSO-only control and quantified gene expression using 3' end labeling. Sequencing libraries were prepared using the Lexogen QuantSeq 3'Forward kit and sequencing of single end reads (1 x 65) was performed on an Illumina HiSeq 4000 at 5M reads per sample. For processed data, reads were aligned against GRCm38 using STAR. Transcripts were quantified and annotated against GencodeM11 using Rsubread. Samples were normalized with CQN. Mouse primary cultures were treated with fatostatin versus DMSO vehicle control; and RNAseq performed using Lexogen QuantSeq 3' Forward kit.