Dataset Information


Microenvironment Cell Populations Affymetrix HuGene 1.0ST

ABSTRACT: Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix HuGene 1.0ST profiles. Sample's annotation is available as supplementary material. Overall design: 3224 gene expression profiles from immune cell populations, non-immune non-malignant cell populations and non-hematopoietic cancer cell lines were gathered from 81 different studies. Data was normalized using the fRMA R package, version 1.18.0, and version 1.0.0. fRMA was applied to single series independantly, and the resulting gene expression matrices were then concatenated.

SUBMITTER: Etienne Becht 

PROVIDER: GSE86357 | GEO | 2016-09-02



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Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression.

Becht Etienne E   Giraldo Nicolas A NA   Lacroix Laetitia L   Buttard Bénédicte B   Elarouci Nabila N   Petitprez Florent F   Selves Janick J   Laurent-Puig Pierre P   Sautès-Fridman Catherine C   Fridman Wolf H WH   de Reyniès Aurélien A  

Genome biology 20161020 1

We introduce the Microenvironment Cell Populations-counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data. We present in vitro mRNA mixture and ex vivo immunohistochemical data that quantitatively support the validity of our method's estimates. Additionally, we demonstrate that MCP-counter overcomes several limitations or weaknesses of previously proposed com  ...[more]