Bone marrow derived macrophages RNA-Seq (WT vs SIRPa KO)

RNA transcriptome difference between WT and SIRPa knockout (KO) bone marrow derived macrophages (BMDMs). To understand how SIRPa inhibits the phagocytotic capacity of macrophages, a mouse lacking SIRPa was generated, and the transcriptional profiles of BMDMs from wild-type and SIRPa KO mice were compared, using RNA sequencing. BMDMs from WT and SIRPa KO mice were generated by growing freshly isolated bone marrow cells for 7 days in medium supplemented with 30% (vol/vol) L929 cell-conditioned medium. Total RNA was isolated from WT and SIRPa KO macrophage using the RNeasy Plus Mini Kit (Cat# 74134, Qiagen). RNA-Seq library preparation was performed using the Illumina TruSeq Stranded mRNA Kit, according to manufacturer’s instructions, and sequenced with Illumina HiSeq 2000 Sequencer. Read quality was confirmed using FastQC v0.10.1 before alignment using TopHat v2.0.10 on the mouse GRCm38/mm10 genome.