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 &lt;0.05, after applying Benjamini-Hochberg correction, was chosen for determining significant differentially expressed genes.<br>Data sheet name: allsymbol.genes.expressionThis 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 <br>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.<br>Data sheet name: WT-vs-HE.genes.filter.annot<br>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.<br><br>

在肾脏移植领域，供体肾脏不可避免地会遭受缺血再灌注损伤（ischemia-reperfusion injury）。探究缺血再灌注损伤的发病机制，并寻找有效手段以减轻缺血再灌注后肾小管急性损伤，具有重要的科研与临床价值。本研究系统分析了3只SHP-1（由Ptpn6编码）缺陷小鼠与3只野生型小鼠的表达谱差异，并通过RNA测序（RNA-sequencing）获取了21367个基因的表达数据。
使用TopHat v2.1.0软件并以默认参数生成可用于Cufflinks的比对结果；随后借助Cufflinks将RNA测序双端读数比对至参考基因组——Ensembl 90版本GRCm38.p5。采用每百万片段每千碱基片段数（FPKM, fragments per kilobase million）对RNA-seq数据中注释基因的表达水平进行量化，FPKM计算公式如下：FPKM = (比对上的片段数) × 10³ × 10⁶ / [(转录本长度) × (总片段数)]。通过对数转换与均值归一化处理表达数据，以用于组间比较。经Benjamini-Hochberg校正后，选取错误发现率（FDR, false discovery rate）<0.05作为筛选显著差异表达基因的判定阈值。
数据表名称：allsymbol.genes.expression
该数据表包含3只SHP-1（由Ptpn6编码）缺陷小鼠与3只野生型小鼠的21367个基因的全部表达数据。
数据表名称：WT-vs-HE.genes.annot
该数据表包含3只SHP-1（由Ptpn6编码）缺陷小鼠与3只野生型小鼠的21367个基因的表达量比较数据。
数据表名称：WT-vs-HE.genes.filter.annot
该数据表包含3只SHP-1（由Ptpn6编码）缺陷小鼠与3只野生型小鼠的161个显著差异表达基因的表达量比较数据。