This study gives a single-cell view of the Pkd1-associated PKD pathology, thus providing a unique cellular-level view of transcriptional alterations associated with Pkd1 heterozygous kidney development and Pkd1 homozygous cyst initiation and progression, which reveals cell-type-specific and shared gene expression perturbations, disease-associated cellular subpopulations and transcriptional responses to cystic microenvironment. The gene discussed is PKD1; the disease is cyst.