Search Tips
Description
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.

From the GEO 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."
Subject of Study
Homo sapiens
Subject(s)
Breast Neoplasms
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Immunotherapy
Lymphocytes, Tumor-Infiltrating
Receptors, Antigen, T-Cell
Transcriptome
Tumor Microenvironment/immunology
Subject Gender
Female
OncoTree Cancer Type(s)
Breast
Access via GEO

RNA and TCR sequencing data
Accession #: GSE114724

Access via SRA

RNA Sequence reads for 10 samples
Accession #: SRP148594

Access via BioProject

Additional information about overall initiative.
Accession #: PRJNA472381

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus database provides open access to these files. SRA and/or tar files can be downloaded directly from the site or viewed in the NCBI SRA Run Selector (link at bottom of page).
Associated Publications
Azizi E, Carr A, Plitas G, et al. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell. 2018; 174(5):1293-1308.e36.
Data Type
Genomic
Equipment Used
Illumina HiSeq 2500

High throughput sequencing system

Nextseq 500 System

Whole Genome Sequencing System

Dataset Format(s)
CSV, TSV, SRA, TAR, MTX
Dataset Size
155.7 Mb (TAR of CSV, MTX, TSV), 112.4 Mb (TSV), 158.8 Gb (SRA)
Other Resources
Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment Superseries

GEO Superseries to which this dataset accession belongs

Data Catalog Record Updated
2021-11-04