Transcriptional Profile of NLRP3-Deficient Cells

The 5637-bladder epithelial cell line (Cas9 controls and NLRP3-deficient cells) was infected with CFT073 for 6 h at a multiplicity of infection (MOI) of 10 at 37 °C with 5% CO₂. Total RNA was isolated from the cells utilizing the E.Z.N.A. Total RNA Kit I (Omega Bio-tek, Norcross, GA, USA). RNA quality and integrity was assessed using the Agilent Tapestation 2200 platform (Agilent Technologies, Palo Alto, CA, USA). The RNA integrity number (RIN) was 10 for all samples. The Low Input Quick Amp WT Labelling Kit (Agilent) was used to label cRNA. Hybridization of labelled cRNA samples was carried out in a G2545A hybridization oven (Agilent) onto Agilent SurePrint G3 (v3) Human Gene Expression 8 × 60 k (Agilent Technologies, Palo Alto, CA, USA) glass arrays. The arrays were then scanned with a G2505C array laser scanner (Agilent Technologies, Palo Alto, CA, USA). The feature Extraction Software (v. 10.7.3.1, Agilent Technologies, Palo Alto, CA, USA) was used for image analysis and data extraction [30 (link)]. Gene expression data is available in the GEO database with the accession number GSE243098.