| Experiment Id | GSE150338 | Name | 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 |
| Experiment Type | RNA-Seq | Study Type | Baseline |
| Source | GEO | Curation Date | 2024-11-06 |
| description | 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/. 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. |
