Transcriptomic analysis in SHP-1 insufficiency mice after renal ischemia-reperfusion injury

It is of great importance to study the pathogenesis of ischemia-reperfusion injury and find effective measures to attenuate acute injury of renal tubules after ischemia-reperfusion. We systematically analyzed differences in the expression profiles of three SHP-1 (encoded by Ptpn6)-insufficient mice and three wild-type mice by RNA-seq.

We achieved the expression data of 21367 genes. TopHat v2.1.0 was used with the default parameters to generate acceptable alignments for Cufflinks, which was used to align the RNA sequencing paired-end reads against the reference genome, Ensembl release 90 GRCm38.p5. The expression of the annotated genes in the RNA-seq data was evaluated in fragments per kilobase million (FPKM) using Cufflinks.