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| Status |
Public on Nov 18, 2020 |
| Title |
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 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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/.
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| 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
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| Contributor(s) |
Chen L, Chou C, Knepper MA |
| Citation(s) |
33769948, 33769951 |
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| Submission date |
May 11, 2020 |
| Last update date |
Mar 28, 2021 |
| Contact name |
Lihe Chen |
| E-mail(s) |
lihe.chen@nih.gov
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| Phone |
3015947152
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| Organization name |
NHLBI
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| Street address |
10 center drive MSC 1603, Building 10, Room 6N318
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (96)
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| Relations |
| BioProject |
PRJNA631784 |
| SRA |
SRP261167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150338_Mouse_TPM_Replicates.txt.gz |
6.5 Mb |
(ftp)(http) |
TXT |
| GSE150338_RAW.tar |
507.4 Mb |
(http)(custom) |
TAR (of TAR) |
| GSE150338_Seurat_IntegrateData.RData.gz |
1.3 Gb |
(ftp)(http) |
RDATA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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