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 <0.05, after applying Benjamini-Hochberg
correction, was chosen for determining significant difference changes in
expression.