Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of high quality RNA samples from human breast adenocarcinoma MCF-7 cells and human skeletal muscle to evalutate the experimental performance of Actichip microarrays

ABSTRACT: To evaluate the experimental performance of Actichip microarrays, a series of 10 repeated hybridisation experiments, including 5 dye swaps, were carried out with optimised target labelling, hybridisation, scanning and data analysis protocols. All the procedures were standardised to limit the impact of experimental bias or biological variations on data. 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. Epithelial cells and muscle tissue were chosen because they express well-characterised sets of cytoskeleton genes, and were anticipated to give well-contrasted differential expression data when analysed with Actichip.

INSTRUMENT(S): GenePix 4000B [Axon Instruments]

ORGANISM(S): Homo sapiens

DISEASE(S): breast adenocarcinoma

SUBMITTER: VALLAR Laurent

PROVIDER: E-MEXP-965 | 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:Approximatively 75% of the genome of S. aureus (“core” genome) are highly conserved between strains, whereas the remaining 25% (“accessory” genome) are composed of variable regions that are mostly composed of mobile genetic elements (MGE), containing virulence and resistance genes. We have developed a composite DNA-microarray (StaphVar Array) which selectively targets 403 genes located on the accessory or core variable genome. Target genes encode antimicrobial resistance factors (35 %), virulence factors (28 %) and adhesins (31%). This microarray was validated with reference strains and used to characterize the genomic DNA of 13 community-acquired methicillin resistant S. aureus (CA-MRSA) strains representative of all the Multilocus Sequence Types (STs) described to date in Belgium. Analysis of gene content of 8 reference strains by the StaphVar Array matched 96 to 99% of the theoretical results. Analysis of CA-MRSA strains showed that 54.4 % of the genes tested were strain-dependent. Strains presented specific exotoxin, enterotoxin, cytolysin and adhesin gene profile by multi-locus sequence typing (MLST) lineage. One exception to these “lineage-specific” gene profile was the variable presence of the Arginin Catabolic Mobile Element (ACME, characteristic of the USA300 clone) within ST8 strains. In conclusion, this novel StaphVar array enables characterization of more than 400 variable resistance and virulence determinants in S. aureus strains. CA-MRSA strains from Belgium displayed extensive diversity in virulence and resistance profile. The presence of the USA 300 clone in our country was confirmed. Although mainly located on MGE, association of virulence genes were highly conserved within strains of the same MLST lineage. CGH microarray was performed on 13 epidemiologically distinct clinical isolates of methicillin resistant S. aureus. S. aureus labeled genomic DNA were hybridized to StaphVar arrays containing 1326 60mer oligonucleotide probes (Eurogentec, Belgium).

Dataset Information

Transcription profiling of high quality RNA samples from human breast adenocarcinoma MCF-7 cells and human skeletal muscle to evalutate the experimental performance of Actichip microarrays

Publications

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

Similar Datasets

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