Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 57
Release date: Nov 21 2014
Last update date: Aug 9 2018
Access: Public
Diseases: Breast Neoplasms
Dataset link Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

Experimental Protocol


58 tumors representing the different molecular subtypes [triple negative (ER-/PgR-/HER2-); HER2 positive (HER2+); luminal A (ER+/HER2-/histological grade 1), luminal B (ER+/HER2-/histological grade 3)] were obtained from patients recruited between 2007 and 2011 at the Institut Jules Bordet. RNA was profiled using the Affymetrix HG-U133 Plus 2.0 chips and sequenced on the Illumina platform, producing ~30 million 50 bp paired-end reads per sample. The reads alignment and expression quantification were performed using the Tophat/Cufflinks pipeline and the Ensembl genome version hg19. The Affymetrix microarray data were normalized using fRMA and probesets were selected based on the JetSet reannotation package. This submission represents the gene expression component of the study only.

Repositories


GEO

GSE43358

ArrayExpress

E-GEOD-43358

BioProject

PRJNA185514

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Contact


David Brown

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