GSE137603
The splicing factor hnRNP M is a critical regulator for innate immune gene expression in macrophages
Purpose: The goals of this study are to compare hnRNP M shRNA knockdown macrophages to scramble shRNA control macrophages in uninfected cells and Salmonella Typhimurium-infecetd cells to unbiasly look at gene expression changes that are regulated by the splicing factor, hnRNP M during resting state and during an innate immune response. Methods: Macrophage mRNA profiles of uninfected and Salmonella Typhimurium-infected hnRNP M knockdown cells lines and SCR shRNA control RAW264.7 macrophages were generated by  sequencing, in triplicate, using Illumina 1.9 system. The sequence reads that passed quality filters were analyzed at the gene expression level with CLC Genomics Workbench 8 with Transcriptomeics Analysis followed by statistical analysi with Empiciral Analysis of DGE and (EDGE test) and Baggerly's test. qRT–PCR validation was performed using SYBR Green assays. Results: Using CLC Genomics Workbench 8 transcriptomics workflow, we mapped about 30 million sequence reads per sample to the mouse genome (GRCm38). Approximately 140 transcripts showed differential expression between the scramble control and hnRNP M knockdown macrophages in uninfected cells, with a fold change =1.5 and p value <0.05. Additionally, ~150 transcripts showed differential expression between the scramble control and hnRNP M knockdown macrophages in Salmonella-Typhimurium cells, with a fold change =1.5 and p value <0.05. Altered expression of genes was confirmed with qRT–PCR, demonstrating the effectiveness of the RNA-seq method. Conclusions: Our study demonstrates hnRNP M-dependent differential gene expression in the context of the innate immune response. Overall design: Transcriptome profiles of uninfected and Salmonella Typhimurium-infected hnRNP M shRNA knockdown and scramble control shRNA knockdown RAW 264.7 macrophages were generated by sequencing, in triplicate, using Illumina 1.9.