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| Status |
Public on Feb 06, 2019 |
| Title |
quanTIseq: quantifying immune contexture of human tumors |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We introduce quanTIseq, a method to quantify the tumor immune contexture, determined by the type and density of tumor-infiltrating immune cells. quanTIseq is based on a novel deconvolution algorithm for RNA sequencing data that was validated with independent data sets. Complementing the deconvolution output with image data from tissue slides enables in silico multiplexed immunodetection and provides an efficient method for the immunophenotyping of a large number of tumor samples.
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| Overall design |
Blood-derived immune-cell mixtures from 9 healthy donors
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| Contributor(s) |
Finotello F, Trajanoski Z |
| Citation(s) |
31126321 |
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Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke Jsselsteijn, Douglas Johnsons, Yaomin Xu, Yu Wang, Melinda E Sanders, Monica V Estrada, Paula Ericsson-Gonzalez, Justin Balko, Noel F de Miranda, Zlatko Trajanoski. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. bioRxiv 223180. doi:10.1101/223180
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| Submission date |
Dec 01, 2017 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Francesca Finotello |
| Organization name |
Biocenter, Medical University of Innsbruck
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| Department |
Division of Bioinformatics
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| Street address |
Innrain 80-82
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| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (9)
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| GSM2871599 |
Blood-derived immune-cell mixture from donor 1 |
| GSM2871600 |
Blood-derived immune-cell mixture from donor 2 |
| GSM2871601 |
Blood-derived immune-cell mixture from donor 4 |
| GSM2871602 |
Blood-derived immune-cell mixture from donor 5 |
| GSM2871603 |
Blood-derived immune-cell mixture from donor 6 |
| GSM2871604 |
Blood-derived immune-cell mixture from donor 7 |
| GSM2871605 |
Blood-derived immune-cell mixture from donor 9 |
| GSM2871606 |
Blood-derived immune-cell mixture from donor 10 |
| GSM2871607 |
Blood-derived immune-cell mixture from donor 12 |
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| Relations |
| BioProject |
PRJNA420735 |
| SRA |
SRP125988 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE107572_raw_count_PBMC_RNAseq.txt.gz |
351.0 Kb |
(ftp)(http) |
TXT |
| GSE107572_tpm_PBMC_RNAseq.txt.gz |
735.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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