Bulk RNA-seq data of control and Dent disease type 1 URECs

This dataset contains processed bulk RNA-seq data generated as part of the study “Urine-derived Human Kidney Tubuloids to Model the Mid/Distal Nephron Phenotype of Dent Disease 1”. Urine-derived renal epithelial cell (UREC) culture Fresh urine collections were obtained from two male Dent disease type 1 patients (#A and #B) and two healthy, age- and sex-matched male donors. For each individual, urine samples were collected at two time points 46 days apart, generating two independent UREC cultures per donor as biological replicates. For one of the controls, this collection was performed at a single time point. Human URECs were isolated using the previously described protocol by Srivastava et al., (2017) and Garcia et al., (2022). Briefly, for UREC isolation, the fresh urine samples were centrifuged at 400 g for 10 min to form a urinary sediment pellet. The pellets were washed with PBS containing antibiotics to minimize the risk of contamination, and resuspended in primary medium [DMEM-F12 (43.6 mL, Gibco), FBS (5 mL; Gibco), 5000 U/mL penicillin/streptomycin (0.7 mL, ThermoFisher Scientific), 250 µg/mL amphotericin B (0.7 mL, Merck) and 50 μL renal epithelium cell growth medium (REGM) SingleQuots (Lonza #CC-4127)] in 12-well plates. After 72 hours, medium was replaced by proliferation hUREC medium [renal epithelium basal medium (REBM; Lonza #CC-3191), renal epithelia cell growth medium (REGM) SingleQuots (Lonza #CC-4127) and 2% FBS]. UREC bulk RNA sequencing The seven UREC cultures generated were used for bulk RNA-seq analysis. Cells were cultured to ∼90% confluence and serum starved for 48 hours, then dissociated using TrypLE (Gibco #12604013), and cell pellets were washed once with PBS and stored at −80°C. These samples were sent to Novogene (Novogene Co., UK), a commercial facility, for RNA extraction and sequencing. Raw sequencing reads were processed by Novogene (Novogene Co., Ltd., UK), including quality trimming, adapter removal, and alignment of clean reads to the human reference genome (GRCh38) using HISAT2 (v.2.0.5) [37]. Quality control of the processed reads was independently verified by us using FastQC (v.0.12.1) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).