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/).本数据集包含经处理的批量RNA测序（bulk RNA-seq）数据，其源自研究《尿液来源的人肾小管类器官模拟Dent病1型的中/远端肾单位表型》。 尿液来源肾上皮细胞（UREC）培养 新鲜尿液采集自2名Dent病1型男性患者（编号A和B）以及2名年龄、性别匹配的健康男性供体。每位供体的尿液样本于两个间隔46天的时间点采集，每位供体可获得2份独立的UREC培养物作为生物学重复。其中1名健康供体仅进行了单次采样。 人类UREC的分离采用此前Srivastava等人（2017）与Garcia等人（2022）报道的方案。简言之，分离UREC时，将新鲜尿液样本以400 g离心10分钟以获得尿沉渣沉淀。用含抗生素的磷酸盐缓冲液（PBS）洗涤沉淀以降低污染风险，随后重悬于基础培养基：DMEM-F12（43.6 mL，Gibco）、胎牛血清（FBS，5 mL；Gibco）、5000 U/mL青霉素/链霉素（0.7 mL，ThermoFisher Scientific）、250 µg/mL两性霉素B（0.7 mL，Merck）以及50 μL肾上皮细胞生长培养基（REGM）SingleQuots（Lonza #CC-4127），接种于12孔板中。培养72小时后，更换为增殖型hUREC培养基：肾上皮基础培养基（REBM；Lonza #CC-3191）、肾上皮细胞生长培养基（REGM）SingleQuots（Lonza #CC-4127）与2% FBS。 UREC批量RNA测序 本研究共获得7份UREC培养物，用于批量RNA-seq分析。将细胞培养至约90%汇合度后进行48小时血清饥饿处理，随后用TrypLE（Gibco #12604013）解离细胞，用PBS洗涤细胞沉淀一次并置于-80℃保存。将上述样本送至商业测序机构Novogene（英国Novogene有限公司）进行RNA提取与测序。 原始测序读段由Novogene（英国Novogene有限公司）完成处理，包括质量修剪、接头去除，以及使用HISAT2（v.2.0.5）[37]将clean reads比对至人类参考基因组GRCh38。我们使用FastQC（v.0.12.1，https://www.bioinformatics.babraham.ac.uk/projects/fastqc/）独立验证了处理后读段的质量控制情况。