Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Platform comparison and transcription profiling using high quality RNA samples purified from human breast adenocarcinoma MCF-7 cells and human skeletal muscle on the Actichip, Affymetrix U1331 2.0 and an academic 70mer oligochip to validate the Actichip

ABSTRACT: To validate Actichip, we compared this microarray with two other well-established oligonucleotide-based platforms. We used 25-mer oligonucleotide commercial chips (Affymetrix, human genome U133A 2.0) and academic arrays prepared with a 70-mer oligonucleotide set (Operon, human whole genome version 2.0). The same series of high quality RNA samples purified from human breast adenocarcinoma MCF-7 cells and from human skeletal muscle was used in our experiments.

ORGANISM(S): Homo sapiens

DISEASE(S): breast adenocarcinoma

SUBMITTER: VALLAR Laurent

PROVIDER: E-MEXP-968 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton.

Muller Jean J Mehlen André A Vetter Guillaume G Yatskou Mikalai M Muller Arnaud A Chalmel Frédéric F Poch Olivier O Friederich Evelyne E Vallar Laurent L

BMC genomics 20070829

<h4>Background</h4>The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and sho ...[more]

PMID: 17727702

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Project description:Methoxyfenozide (RH-2485) represents the group of non-steroidal ecdysteroid agonists with a dibenzoylhydrazine structure, that are used as novel biorational insecticides in the control of insect pests. Here we report on the selection of Drosophila melanogaster S2 cells for resistance to inhibition of cell proliferation by methoxyfenozide by ~1000-fold over 4 months. Cells were exposed to gradually increasing concentrations of methoxyfenozide and selected out based on the ecdysteroid-sensitive response for cell proliferation. In the resistant cells, the ecdysteroid receptor (EcR/USP) complex was no longer active in the presence of methoxyfenozide. But when resistant cells were relaxed from pressure in methoxyfenozide-free medium, induction of the reporter construct was observed. In parallel, EcR/USP functionality was also restored when resistant cells were rescued by a Drosophila EcR plasmid. However, it was striking that in the resistant cells the ecdysteroid-sensitive response for cell proliferation was not restored upon methoxyfenozide withdrawal, indicating permanent changes in the physiology of the cells during selection. To investigate changes in gene expression caused by inactivation of the EcR/USP complex in resistant cells, Drosophila oligo 14kv1 microarrays were used and probed with cDNAs from resistant cells in the presence and absence of ecdysone agonist on one hand and from unselected sensitive cells on the other hand. A selection of 324 differentially expressed genes was assigned covering diverse functions as transport, enzyme activity, cytoskeleton organization, cell cycle machinery, transcription/translation and ecdysteroid signaling. Besides the identification of (primary and secondary) target genes of the EcR/USP signaling pathway, this analysis is also predicted to gain insights into the mechanism of resistance and the crosstalk between ecdysteroid signaling and cell proliferation-linked processes. In this microarray experiment three biological conditions were under study: (i) untreated S2 cells (S2), (ii) a subpopulation of these untreated cells, which were grown under continuous pressure of methoxyfenozide and which were shown to become resistant to this compound (S2res) and (iii) a subpopulation of the resistant cells, which were again cultured without methoxyfenozide added to the medium (S2res-woMF). For each condition, two subpopulations (which were treated as biological replicates, although they are not exactly independent), were isolated and used for the RNA extractions. The overall experimental design was an n+2 A-optimal design. When each hybridisation is respresented by an arrow (Cy5 ? Cy3), the design can be respresented as follows: First loop = S2.1 ? S2res.1 ? S2.2 ? S2res.2 ? S2.1; Second loop = S2.1 ? S2res-woMF.1 ? S2.2 ? S2res-woMF.2 ? S2.1 (numbers following the condition name correspond to the biological replicate numbers). The two loops are thus connected by S2.1 and S2.2. Two analyses were performed: S2res compared to S2 and S2res-woMF compared to S2.

Dataset Information

Platform comparison and transcription profiling using high quality RNA samples purified from human breast adenocarcinoma MCF-7 cells and human skeletal muscle on the Actichip, Affymetrix U1331 2.0 and an academic 70mer oligochip to validate the Actichip

Publications

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton.

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