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Series GSE158803 Query DataSets for GSE158803
Status Public on Oct 27, 2020
Title A Single-Cell Tumor Immune Atlas for Precision Oncology
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell resolved tumor immune cell atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we developed SPOTlight, a computational tool that identified striking spatial immune cell patterns in tumor sections. We expect the atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification strategies for prognosis and immuno-therapy response.
 
Overall design Single-cell RNA sequencing was performed on two human uveal melanoma cancers, one human ovarian cancer, one human uveal melanoma liver metastasis, one human non-small cell lung cancer brain metastasis (including TCR), two human head and neck cancers and two mice colorectal cancers (one full and one only T cells and TCR)
 
Contributor(s) Nieto P, Heyn H
Citation(s) 34548323
Paula Nieto, Marc Marc Elosua-Bayes, Juan Luis Trincado, Domenica Marchese, Ramon Massoni-Badosa, Maria Salvany, Ana Henriques, Elisabetta Mereu, Catia Moutinho, Sara Ruiz, Patricia Lorden, Vanessa Chin, Dominik Conrad Kaczorowski, Chia-Ling Chan, Richard Gallagher, Angela Chou, Ester Planas-Rigol, Carlota Rubio-Perez, Ivo Glynne Gut, Joseph Maria Piulats, Joan Seoane, Joseph Powell, Eduard Batlle, and Holger Heyn. A Single-Cell Tumor Immune Atlas for Precision Oncology. bioRxiv 2020.10.26.354829; doi:10.1101/2020.10.26.354829
Submission date Sep 30, 2020
Last update date Oct 13, 2021
Contact name Paula Nieto
E-mail(s) nietogarciapaula@gmail.com
Organization name CNAG
Department CNAG
Lab Single-Cell Genomics
Street address Barcelona, Barcelona Science Park - Tower I
City Barcelona
State/province Spain
ZIP/Postal code 08028
Country Spain
 
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (10)
GSM4810687 brain metastasis
GSM4810688 liver metastasis, patient 1
GSM4810689 liver metastasis, patient 1, CD45 enriched
Relations
BioProject PRJNA666613
SRA SRP285894

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
GSE158803_RAW.tar 122.8 Mb (http)(custom) TAR (of CSV, MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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