Fig. 1

Overall experimental design and workflow. a Kidney cortex tissues were obtained from five male patients with kidney cell carcinoma or transitional cell carcinoma scheduled for total nephrectomy. The base-line expression was analyzed under normal condition or pre-ischemia. Gun biopsy was performed for ischemia after 15 min of ischemia and 10 min later, the biopsy was repeated for reperfusion. b Bioinformatic workflow: FastQC for quality assessment and Salmon were executed for RNA-seq quantification from pre-ischemia, ischemia, and reperfusion conditions. Differential expression analysis and self-organizing map (SOM) followed by pathway analysis were performed in parallel to identify key genes and pathways significantly associated with ischemia-reperfusion