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| Status |
Public on Mar 03, 2020 |
| Title |
Single Cell Transcriptomics identifies Focal Segmental Glomerulosclerosis Remission Endothelial Biomarker |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Intrinsic nephron cell types and tissue resident immune cells were recovered from renal biopsy specimens using a scRNAseq protocol for the Kidney Precision Medicine Project (KPMP), designed for deployment in a multicenter research network. Combined processing of 24 samples including 16 tumor-nephrectomy, 5 surveillance and 3 pre-perfusion biopsies using the scRNAseq protocol yielded 22,268 cells (4690 from surveillance biopsies, 16,491 from tumor-nephrectomies and 2834 cells from pre-perfusion biopsies) .
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| Overall design |
scRNA-seq: Using multiple sources of healthy kidney tissue samples, we generated 22,268 single cell profiles. Unbiased clustering resulted in 31 distinct cell clusters that were successfully linked to intrinsic kidney and immune cell types using specific cell markers. In silico assignment of the three endothelial cell clusters to distinct vascular beds were confirmed by in situ hybridization. Transcripts defining the glomerular endothelial cluster (GEC) were evaluated in biopsies from patients with ten different glomerular diseases in the NEPTUNE and ERCB studies. Focal segmental glomerulosclerosis (FSGS) samples were associated with higher GEC scores.
bulk RNA-seq: Transcripts defining the glomerular endothelial cluster (GEC) were evaluated in biopsies from patients with FSGS glomerular diseases in the NEPTUNE cohort studies.
***The submitters are not legally permitted to submit the raw data to GEO or a restricted-access database such as dbGaP or EGA. Therefore, raw data is not provided ****
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| Contributor(s) |
Menon R, Kretzler M |
| Citation(s) |
32107344, 33568476 |
| Submission date |
Nov 25, 2019 |
| Last update date |
Jun 27, 2022 |
| Contact name |
Rajasree Menon |
| E-mail(s) |
rajmenon@umich.edu
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| Phone |
7346159720
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| Organization name |
University of Michigan
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| Department |
Department of Computational Medicine and Bioinformatics
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| Street address |
4544E, MSRB2, Catherine Street, University of Michigan
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| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (92)
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| Relations |
| BioProject |
PRJNA591621 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140989_KPMP_Premiere_reference_SCT_Normalizeddata.txt.gz |
31.8 Mb |
(ftp)(http) |
TXT |
| GSE140989_RAW.tar |
408.5 Mb |
(http)(custom) |
TAR (of MTX, TSV, TXT) |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data not provided for this record |
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