Mutations in the PKD1 or PKD2 genes are the cause of autosomal dominant polycystic kidney disease (ADPKD). The encoded proteins localize within the cell membrane and primary cilia and are proposed to be involved in mechanotransduction. Therefore, we evaluate shear stress dependent signaling in renal epithelial cells and the relevance for ADPKD. Using RNA sequencing and pathway analysis, we compared gene expression of in vitro shear stress treated Pkd1^−/− renal epithelial cells and in vivo pre-cystic Pkd1del models. We show that shear stress alters the same signaling pathways in Pkd1^−/− renal epithelial cells and Pkd1^wt controls. However, expression of a number of genes was slightly more induced by shear stress in Pkd1^−/− cells, suggesting that Pkd1 has the function to restrain shear regulated signaling instead of being a mechano-sensing activator. We also compared altered gene expression in Pkd1^−/− cells during shear with in vivo transcriptome data of kidneys from Pkd1^del mice at three early pre-cystic time-points. This revealed overlap of a limited number of differentially expressed genes. However, the overlap between cells and mice is much higher when looking at pathways and molecular processes, largely due to altered expression of paralogous genes. Several of the altered pathways in the in vitro and in vivo Pkd1^del models are known to be implicated in ADPKD pathways, including PI3K-AKT, MAPK, Hippo, calcium, Wnt, and TGF-β signaling. We hypothesize that increased activation of selected genes in renal epithelial cells early upon Pkd1 gene disruption may disturb the balance in signaling and may contribute to cyst formation.