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Series GSE79338 Query DataSets for GSE79338
Status Public on May 18, 2016
Title The Glioma-Infiltrating T Cell Receptor Repertoire
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary While immune signaling has emerged as a defining feature of the glioma microenvironment, local selection of responding T cells and their anti-tumor potential as a population are difficult to measure directly in patients. High-throughput sequencing of T cell receptor repertoires (TCRseq) provides a population-wide statistical description of how T cells respond to disease. Here, we define new immunophenotypes in glioma based on TCRseq and RNA-Seq of tumor tissue, non-neoplastic brain tissue, and peripheral blood from patients. Using information theory, we characterize antigen-driven selection in glioma and its relationship with the expression of distinct immune-functional pathways in the tumor microenvironment. Finally, we identify a strong relationship between usage of certain TCR in peripheral blood and the divergence of the infiltrating T cell population from the peripheral repertoire. We anticipate that these immunophenotypes will be foundational to monitoring and predicting response to anti-glioma vaccines and immunotherapy.
Overall design We characterized the T cell receptor (TCR) repertoires of 11 high-grade glioma patients, three low-grade glioma patients, and thee non-glioma patients by TCRseq of brain-infiltrating T cells and matching peripheral blood. In addition, we obtained gene expression profiles from brain tissue of each patient by RNA-Seq. We additionally measured the TCR repertoires exclusively from peripheral blood of one additional non-glioma patient.
Contributor(s) Sims PA
Citation(s) 27261081
Submission date Mar 17, 2016
Last update date May 15, 2019
Contact name Peter A Sims
Organization name Columbia University
Street address 3960 Broadway, Lasker 203AC
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (75)
GSM2092506 TCR45A.BC3
GSM2092507 TCR44B.BC4
GSM2092508 TCR44A.BC1
BioProject PRJNA315543
SRA SRP071932

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE79338_BrainRNAseq.txt.gz 1.7 Mb (ftp)(http) TXT
GSE79338_RAW.tar 229.8 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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