E-MEXP-467 - Platform comparison and transcription profiling of human cell lines on three array platforms (Affymetrix GeneChip Human Genome U133 Plus 2.0, GE Healthcare/Amersham Biosciences UniSet Human 20K I Bioarray and Agilent Whole Human Genome Oligo Microarray)

Status
Released on 1 November 2005, last updated on 3 May 2014
Organism
Homo sapiens
Samples (4)
Arrays (3)
Protocols (12)
Description
A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChipTM, GE Healthcare CodeLinkTM and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program. The analyses were based on data from three biologically distinct human cell lines and a non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Raw data from the following were studied : 12 Affymetrix HG-U133 plus 2.0 GeneChipTM arrays (3 arrays per sample type independently labeled, March, 2004); 12 Agilent's "44K whole genome" arrays (4 arrays per cell line; 3 arrays for 3 independent labeling reactions plus one technical replicate, June 2004); 12 Amersham CodeLinkTM UniSet Human 20K Human arrays (3 slides per sample type labeled in batch, March, 2004).
Experiment types
transcription profiling by array, hardware variation
Contacts
Fabien Petel <PetelF@ligue-cancer.net>, Aurélien de Reyniès, Daniela Geromin, David S Rickman, François Sigaux, Jean-Michel Cayuela, Philippe Dessen
Citation
Comparison of the latest commercial short and long oligonucleotide microarray technologies. Aurelien de Reynies; Daniela Geromin; Jean-Michel Cayuela; Fabien Petel; Philippe Dessen; Franncois Sigaux; David Rickman.
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