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Series GSE159115 Query DataSets for GSE159115
Status Public on May 22, 2021
Title Single Cell Analyses of Renal Cell Cancers Reveal Insights into Tumor Microenvironment, Cell of Origin, and Therapy Response
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Diverse subtypes of renal cell carcinomas (RCC) display a wide spectrum of histomorphologies, proteogenomic alterations, immune cell infiltration patterns, and clinical behavior. Delineating the ontogeny of these malignancies with the identification of cells of origin for different RCC subtypes will provide mechanistic insights into their diverse pathobiology. With this aim, we performed single cell RNA sequencing (scRNA-seq) analysis of ~30,000 cells dissociated from benign human kidney and renal tumor specimens. The benign renal tissue cell atlas comprised 26 distinct cell clusters representing all known major and minor cell types, as well as two rare proximal tubule cell types (PT-B and PT-C) and one novel entity containing both intercalated and principal cell (IC-PC) phenotypes. In comparison, the tumor cell atlas was comprised of 13 different cell clusters encompassing neoplastic cells and components of the tumor microenvironment. Using a random forest model trained on the scRNA-seq data from benign tubular epithelial cell types, we predicted the putative cell of origin for more than 10 different RCC subtypes.
 
Overall design Single-cell suspensions from 8 renal tumor specimens and 6 benign human kidney specimens from clear cell cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) patients were obtained by enzymatic dissociation. The cell suspension was used to prepare single cell RNA-seq libraries using the 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).

*** This GEO submission contains only processed data (raw counts tables in HDF5 format), raw data (FASTQ files) will be submitted to dbGaP/SRA due to to patient privacy concerns.

The cell annotation file *csv files were added on Sep 23, 2022.
 
Contributor(s) Zhang Y, Narayanan SP, Dhanasekaran SM, Raskind G, Wang X, Vats P, Mannan R, Su F, Wang L, Cao X, Kumar-Sinha C, Giordono TJ, Morgan TM, Pitchaya S, Alva A, Mehra R, Cieslik M, Chinnaiyan AM
Citation(s) 34099557
Submission date Oct 06, 2020
Last update date Sep 23, 2022
Contact name Arul M. Chinnaiyan
Organization name University of Michigan
Street address 1500 E. Medical Center Dr
City Ann Arbor
State/province MICHIGAN
ZIP/Postal code 48109
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (14)
GSM4819725 SI_18854
GSM4819726 SI_18856
GSM4819727 SI_18855
Relations
BioProject PRJNA667716

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE159115_RAW.tar 115.0 Mb (http)(custom) TAR (of H5)
GSE159115_ccRCC_anno.csv.gz 905.6 Kb (ftp)(http) CSV
GSE159115_chRCC_anno.csv.gz 111.5 Kb (ftp)(http) CSV
GSE159115_normal_anno.csv.gz 271.0 Kb (ftp)(http) CSV
Raw data not provided for this record
Processed data provided as supplementary file

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