NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE202813 Query DataSets for GSE202813
Status Public on Jul 17, 2023
Title Single-cell analysis of immune and stroma cell remodeling in renal cell carcinoma primary tumors and bone metastatic lesions
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Cancer metastasis in the bone represents an incurable disease. About one-third of patients with advanced renal cell carcinoma (ccRCC) have bone metastasis at the time of diagnosis making it a life-threatening disease. The bone metastatic niche, including immune and stroma microenvironment, has not been defined. Here, we created a human single-cell transcriptome cell-atlas of ccRCC bone metastases, contrasted with normal bone marrow immune cells and stroma.
 
Overall design We collected fresh patient samples directly from the operating room and performed single-cell transcriptomic profiling of solid metastatic tissue (Tumor fraction), liquid bone marrow at the vertebral level of spinal cord compression (Involved), as well as liquid bone marrow from a different vertebral body distant from the tumor site but within the surgical field (Distal). In addition, we enriched immune and stroma cells from patients undergoing hip replacement surgery (Benign) as extra control. Bone marrow were disaggregated and profiled by 10X Genomics Single cell 3 gene expression V2.
 
Contributor(s) Mei S
Citation(s) 38281962
Submission date May 11, 2022
Last update date Feb 14, 2024
Contact name Shenglin Mei
E-mail(s) samleomei@gmail.com
Organization name Harvard medical school (DMBI)
Street address 10 Shattuck Street
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (33)
GSM6133738 RCC-BM10-Tumor
GSM6133739 RCC-BM10-Involve
GSM6133740 RCC-BM10-Noninvolved
Relations
BioProject PRJNA837343

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
GSE202813_RAW.tar 144.2 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap