GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE114724 Query DataSets for GSE114724
Status Public on Jun 28, 2018
Title Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph node. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer, with important implications for characterizing tumor-infiltrating immune cells. 
Overall design Single-cell RNA sequencing was performed on three patients using the 10x genomics TCR profiling kits. For each patient, populations of T-cells were assayed for both TCR sequence and trancriptome-wide RNA-sequence. Two donors have a replicate experiment.
Contributor(s) Azizi E, Carr AJ, Plitas G, Cornish AE, Konopacki C, Prabhakaran S, Nainys J, Wu K, Kiseliovas V, Setty M, Choi K, Fromme RM, Dao P, McKenney PT, Wasti RC, Kadaveru K
Citation(s) 29961579
Submission date May 21, 2018
Last update date Mar 27, 2019
Contact name Ambrose J Carr
Organization name Memorial Sloan Kettering Cancer Center
Department Computational and Systems Biology Program, SKI
Lab Dana Pe'er
Street address 417 E 68th St
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (10)
GSM3148575 BC09_TUMOR1
GSM3148576 BC09_TUMOR2
GSM3148577 BC10_TUMOR1
This SubSeries is part of SuperSeries:
GSE114727 Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
BioProject PRJNA472381
SRA SRP148594

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
GSE114724_RAW.tar 155.7 Mb (http)(custom) TAR (of CSV, MTX, TSV)
GSE114724_rna_imputed.tsv.gz 57.2 Mb (ftp)(http) TSV
GSE114724_rna_raw.tsv.gz 55.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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