GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE75688 Query DataSets for GSE75688
Status Public on Dec 09, 2016
Title Single cell RNA sequencing of primary breast cancer.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We performed single cell RNA sequencing (RNA-seq) for 549 primary breast cancer cells and lymph node metastases from 11 patients with distinct molecular subtypes (BC01-BC02, estrogen receptor positive (ER+); BC03, double positive (ER+ and HER2+); BC03LN, lymph node metastasis of BC03; BC04-BC06, human epidermal growth factor receptor 2 positive (HER2+); BC07-BC11, triple-negative breast cancer (TNBC); BC07LN, lymph node metastasis of BC07) and matched bulk tumors. We separated these single cells into epithelial tumor and tumor-infiltrating immune cells using inferred CNVs from RNA-seq. The refined single cell profiles for the tumor and immune cells provide key expression signatures of breast cancer and the surrounding microenvironment.
Overall design All single-cell mRNA expression profiles were acquired from eleven patients (BC01-BC11) including two lymph node metastases (BC03LN, BC07LN) (549 samples). We applied four filtering criteria so as to remove samples with low sequencing quality and finally obtained 515 single cell sequencing data. Matched bulk tumor tissues and/or pooled cells were also sequenced and analyzed by the single cell RNA-seq pipeline (14 samples). Bulk tumor transcriptomes showed significant correlations with the average of single cell transcriptomes.
Contributor(s) Chung W, Eum HH, Lee H, Han W, Park W
Citation(s) 28474673
Submission date Dec 03, 2015
Last update date May 15, 2019
Contact name Woosung Chung
Organization name Samsung Genome Institute
Street address Samsung Medical Center
City Seoul
State/province State...
ZIP/Postal code ASI|KR|KS013|SE
Country South Korea
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (563)
GSM1963742 BC01_Pooled
GSM1963743 BC01_Tumor
GSM1963744 BC04_Pooled
BioProject PRJNA305054
SRA SRP066982

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
GSE75688_GEO_processed_Breast_Cancer_raw_TPM_matrix.txt.gz 10.3 Mb (ftp)(http) TXT
GSE75688_final_sample_information.txt.gz 1.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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