Fig. 1

Overview of experiments performed in this study. All experiments were carried out in biological triplicate using three kidneys from three different mice. a 37 °C dissociation used the Multi-tissue dissociation kit 2 from Miltenyi Biotec. b Cold dissociation was carried out on ice using B. Licheniformis protease. In a and b, methanol-fixed samples used 80% MeOH at − 20 °C and then were stored at − 80 °C. Cryopreservation was carried out using 50% FBS, 40% RPMI-1640, 10% and DMSO with gradient cooling to − 80 °C then stored in liquid nitrogen. c–e Whole kidneys were flash frozen using an isopentane bath − 30 °C and then stored at − 80 °C. Three different nuclei preparation methods were tested using either fluorescently activated nuclei sorting (FANS) or a sucrose gradient to enrich for singlet nuclei. f Bulk RNA-seq was carried out using the NEBNext Ultra II RNA Library Kit for Illumina with rRNA depletion or NEBNext Poly(A) mRNA isolation module. See “Methods” for more details