Targeted single-cell RNA-seq identifies minority cell types of kidney distal nephron & A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse

Characterization of gene expression for each renal cell type is essential for identifying mechanisms underlying kidney physiology and pathophysiology. Here, we built a transcriptome landscape mouse renal epithelial cells by deep sequencing of all 14 mouse renal segments, upon which we developed an enrichment protocol to characterize distal nephron cells by single-cell RNA-seq. Our renal tubule expression atlas provided landscapes of gene expression and alternative splicing along the renal tubule segments. We identified, and integrated segment-specific genes with human gene nomenclature to understand the gene function and conservation. We further developed an enrichment strategy for single-cell analysis of distal nephron cells. The analysis revealed heterogeneous gene expression in DCT1-DCT2-CNT. Moreover, we identified two mosaic cell types in thick ascending limb and verified their presence in mouse kidney tissue. Our data provides a rich resource for kidney research and we provide our data user-friendly at https://esbl.nhlbi.nih.gov/MRECA/Nephron/ and https://esbl.nhlbi.nih.gov/MRECA/DCT/. Overall design: To quantify the gene expression, we carried out ultra-low input RNA-Seq in each of the 14 renal tubule segments plus glomerulus from male mouse kidneys. Samples were collected from at least 3 mice (6- to 8-week-old). In total, we analyzed 93 samples from 53 mice (87 renal tubules plus 6 glomeruli). For single-cell RNA-seq, we dissociated the mouse renal cortical tissue into single-cell suspensions using a cold-active protease followed by cell enrichment for scRNA-seq on 10X Chromium platform. We carried out 3 independent runs with 3000-6000 cells each as input Definitions: PTS1, initial segment of the proximal convoluted tubule PTS2, proximal straight tubule in cortical medullary rays PTS3, last segment of the proximal straight tubule in outer stripe of outer medulla DTL1, short descending limb of the loop of Henle DTL2, long descending limb of the loop of Henle in the outer medulla DTL3, long descending limb of the loop of Henle in the inner medulla ATL, thin ascending limb of the loop of Henle MTAL, medullary thick ascending limb of the loop of Henle CTAL, cortical thick ascending limb of the loop of Henle DCT, distal convoluted tubule CNT, connecting tubule CCD, cortical collecting duct OMCD, outer medullary collecting duct IMCD, inner medullary collecting duct