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Series GSE73121 Query DataSets for GSE73121
Status Public on Sep 18, 2015
Title Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Clear cell renal cell carcinoma (ccRCC) initiated from the renal epithelium is the most prevalent histological type of adult kidney cancers. Dissecting intratumoral heterogeneity (ITH) of ccRCC has leveraged to extend our knowledge on how primary tumors harboring driver mutations evolve and spread to other sites. The cellular fractions within and across the primary (pRCC) and metastatic RCC (mRCC) are heterogeneous in both their genetic and biological features determining the variability in clinical aggressiveness and sensitivity to the therapy. To achieve sustainable therapeutic benefit with targeted agents in mRCC, the effective target should focus on signaling pathways that are related to driver mutations occurred early in the clonal evolution of the disease and thus should be common to primary tumor and metastatic sites. Considering that extensive genetic heterogeneity may result in drug response variability among patients and treatment resistance, the tailored strategies for metastatic RCC is urgently needed. Here, we analyze single-cell RNA-seq (scRNA-seq) data from a matched primary RCC (pRCC) and lung metastasis (mRCC) to dissect ITH at the highest resolution to date with the objective of discovering the better therapeutic regimen.
 
Overall design In order to identify successful clonal propagation from patient to PDX samples and understand pathogenesis from primary to metastatic RCC, we performed whole-exome sequencing (WES, n=4) and matched aCGH (n=4) on bulk tumor samples. And we utilized single-cell RNA sequencing (scRNA-seq) to model and dissect functional heterogeneity acroass primary and metastatic RCC tumors. We checked whether of capturing live one cell, not more cells, in microfluidics by fluorescent microscopic observation. To construct RNA sequencing libraries, we performed further quality controls including adequate quantities and qualities of amplified transcriptomes respectively from single cells. Tumor cells from the parental mRCC (n=34), PDX-mRCC (n=36) and PDX-pRCC (n=46) were finally analyzed in this study after filtering out poor quality cells.
 
Contributor(s) Kim K, Lee HW, Lee H, Joo KM, Park W
Citation(s) 27139883
Submission date Sep 17, 2015
Last update date May 15, 2019
Contact name Kyu-Tae Kim
Organization name Samsung Medical Center
Department Samsung Genome Institute
Street address Irwon-Ro 81
City Seoul
ZIP/Postal code 135-710
Country South Korea
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (121)
GSM1887215 PDX_mRCC_Pooled
GSM1887216 PDX_mRCC_SC_01
GSM1887217 PDX_mRCC_SC_03
This SubSeries is part of SuperSeries:
GSE73122 Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells
Relations
BioProject PRJNA296119
SRA SRP063840

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
GSE73121_RAW.tar 162.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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