Proteomic analysis of Cdkal1-KO mouse podocyte cell line

E11 murine kidney podocyte cell line was purchased from Cell Lines Service. Cells were cultured in RPMI medium (Wako) supplemented with 10% fetal bovine serum (Sigma) at 33°C and induced to differentiate by culture at 37°C for two weeks and 5% CO2. Cdkal1 knockout in the E11 cell line was performed using a guide RNA targeting exon 5 of Cdkal1 followed by cloning into the Lenti-CRISPR v2 vector (Addgene). The cell lysates were digested by trypsin by phase-transfer surfactant method. The digested samples were desalted and reconstituted with 0.1% trifluoroacetic acid after drying. The digested peptide samples corresponding to 1 ug protein were injected into liquid chromatography-tandem mass spectrometry. The data acquired by SWATH modes on TripleTOF6600 (SCIEX, Framingham, MA, USA) with the Eksigent NanoLC400 system (SCIEX). Proteins were identified and quantified with DIA-NN 1.8 with UniProt Human reference proteome data.