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

In kidney transplantation, the donor kidney inevitably undergoes 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. The following formula was used to calculate the FPKM value: FPKM = (number of mapped fragments) × 10³ × 10⁶/ [(length of transcript) × (total number of fragments)]. Log transformation and zero-mean normalization were used to normalize the expression data for comparisons. The false discovery rate (FDR) of &lt;0.05, after applying Benjamini-Hochberg correction, was chosen for determining significant difference changes in expression.<br>