After reads filtering, clean reads were mapped to reference transcripts using Bowtie2, and then, gene expression level was calculated with RNA-seq by Expectation-Maximization (RSEM). On the basis of the gene expression level, differential expression genes were identified using DESeq2 algorithms. Fold change of ≤−2 or ≥2 and adjusted P < 0.05 were considered significantly differentially expression. Gene ontology analysis was performed using DAVID 6.8. FP-rescued genes were defined as either (i) genes whose expressions in FP-treated Pkd1−/− mice were returned to levels in WT mice (≤1.5-fold increase in FP-treated Pkd1−/− versus WT mice, adjusted P < 0.05) or (ii) genes whose expressions were restored ≥50% (adjusted P < 0.05) after FP treatment (Pkd1−/− versus FP-treated Pkd1−/− mice).

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