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

ORGANISM(S): uncultured organism

SUBMITTER: Peyret Pierre 

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

REPOSITORIES: biostudies-arrayexpress