Transcriptional Analysis of Wild Type and KLF2-/- Peritoneal Macrophages

Krüppel-like factor 2 (KLF2) is a critical regulator of monocyte activation in response to inflammatory stimuli. Here, we report transcriptomic differences in peritoneal macrophages isolated from Lysozyme M Cre (control) and myeloid-specific KLF2 knockout mice. Peritoneal macrophages were isolated from lysozyme M Cre (wt) and myeloid-specific KLF2 knockout (k2) mice 72 hours after thioglycolate injection. Three mice per group were used. cDNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit and sequenced on a Illumina HiSeq 2500 platform. Reads from each sample were aligned to the mouse genome (UCSC mm10) using TopHat2 (Kim et al., 2013). Macrophage gene expression was quantitated as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (Trapnell et al., 2010).