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Experimental validation of HiSpOD probe design with complex background mRNA or 3 known antiense RNA and expression analysis on a contaminated groundwater sample


ABSTRACT: HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 M-BM-5g of labelled aRNA from sheep rumen content (background aRNA). Secondly, hybridization of 1011 copies of labelled aRNA derived from in vitro transcription of three synthetic genes (mmoC, vcrA and tceA) and mixed with 6 M-BM-5g of the same complex background material were performed to test their sensibility. Finally, the expression analysis of a contaminated groundwater sample was performed. A 3 chip study was realized. The first one is a negative control performed with a complex background material (labelled antisense mRNA from sheep rumen content). The second one is a positive control realized with labelled antisense RNA derived from in vitro transcription of three synthetic genes mixed the same complex background material. The third consists in the hybridization of antisense mRNA retrieved from a contaminated groundwater. Each probe (3392) was synthetized in triplicate, and a total of 8,863 random probes was used to determine the background noise.

ORGANISM(S): uncultured organism

SUBMITTER: Peyret Pierre 

PROVIDER: E-GEOD-21492 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

HiSpOD: probe design for functional DNA microarrays.

Dugat-Bony Eric E   Missaoui Mohieddine M   Peyretaillade Eric E   Biderre-Petit Corinne C   Bouzid Ourdia O   Gouinaud Christophe C   Hill David D   Peyret Pierre P  

Bioinformatics (Oxford, England) 20110106 5


<h4>Motivation</h4>The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays.<h4>Results</h4>We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual  ...[more]

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