Transcriptomic analysis in three SHP-1 insufficiency mice and three wide type 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 and achieved the expression data of 21367 genes by RNA-sequencing.
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 differentially expressed genes.

Data sheet name: allsymbol.genes.expression
This data sheet include the whole expression data of 21367 genes in three SHP-1 (encoded by Ptpn6)-insufficient mice and three wild-type mice.
Data sheet name: WT-vs-HE.genes.annot

This data sheet include the comparasion of expression data of 21367 genes in three SHP-1 (encoded by Ptpn6)-insufficient mice and three wild-type mice.

Data sheet name: WT-vs-HE.genes.filter.annot

This data sheet include the comparasion of expression data of 161 significant differentially expressed genes in three SHP-1 (encoded by Ptpn6)-insufficient mice and three wild-type mice.