Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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)

ABSTRACT: 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).

INSTRUMENT(S): G2565BA DNA microarray scanner [Agilent], GenePix 4000B [Axon]

ORGANISM(S): Homo sapiens

DISEASE(S): breast cancer

SUBMITTER: Fabien Petel

PROVIDER: E-MEXP-467 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comparison of the latest commercial short and long oligonucleotide microarray technologies.

de Reyniès Aurélien A Geromin Daniela D Cayuela Jean-Michel JM Petel Fabien F Dessen Philippe P Sigaux François F Rickman David S DS

BMC genomics 20060315

<h4>Background</h4>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 GeneChip, GE Healthcare CodeLink and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program.<h4>Results</h4>All wet-lab experiments and raw data acquisitions were performed independently by each commercial platf ...[more]

PMID: 16539734

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Project description:15-Lipoxygenase 2 (15-LOX2), a human-specific lipid-peroxidizing enzyme, is mainly expressed in luminal compartment of the normal prostate and often decreased or lost in prostate cancer (PCa). Previous studies from our lab implicate 15-LOX2 as a functional tumor suppressor. To better understand the biological role of 15-LOX2 in vivo, we established prostate-specific 15-LOX2 transgenic mice using the ARR2PB promoter. Unexpectedly, 15-LOX2 expression resulted in age-dependent prostatic hyperplasia. Interestingly, transgenic expression of 15-LOX2sv-b, a splice variant that lacks the arachidonic acid metabolizing activity, also induced hyperplasia and enlargement of the prostate. Prostatic hyperplasia induced by both 15-LOX2 and 15-LOX2sv-b was associated with an increase in proliferative (i..e., Ki67+) and luminal cells but 15-LOX2-induced hyperplasia was also accompanied by a prominent increase in basal cells. Microarray analysis revealed distinct gene expression profiles that could help explain the prostate phenotypes. Strikingly, 15-LOX2 (but not 15-LOX2sv-b) transgenic prostate showed up-regulation of several well-known stem/progenitor cell molecules including Sca-1, Trop2, p63 and Psca. Prostatic hyperplasia caused by both 15-LOX2 and 15-LOX2sv-b did not progress to PCa over >5 years of observations. Mechanistically, hyperplastic prostate lobes (especially those of the 15-LOX2 mice) showed a dramatic increase in senescent cells revealed by increased SA-ßgal, HP1, and p27Kip1 staining. Collectively, our results suggest that 15-LOX2 expression in mouse prostate leads to hyperplasia that activates the senescence checkpoint, which may in turn function as a barrier to tumor development. RNA was isolated from combined prostatic lobes of 6 mice (to reduce inter-animal variation) from ~2.5 month old (young; y) 15-LOX2 (line fl26), 15-LOX2sv-b (line svb9), wild type (wt) and ~15 month old (old; o) wt mice and hybridized onto Agilent's whole mouse genome oligoarrays arrays (G4122A) in fl26y(vs)wty, svb9y(vs)wty and wto(vs)wty combinations. The hybridizations were carried out in duplicates using an independent set of samples (biological replicates).

Dataset Information

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)

Publications

Comparison of the latest commercial short and long oligonucleotide microarray technologies.

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