Small RNAs profiling by using microarray with custom-designed probes
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ABSTRACT: We designed a group of probes for detection of known and some putative E. coli sRNAs and included them in a commercial microarray containing a standard set of probes developed by Agilent Technologies for hybridization with E. coli transcripts. To assess the potential of the re-designed microarray to detect E. coli sRNAs, RNA profiling experiments were performed with total RNA extracted from E. coli MG1655 cells in log phase, grown in rich (Luria-Bertani) and minimall (M9/Glucose) media. The microarray data obtained indicate that many sRNAs could yield reasonably strong signals (i.e. considerably above the background). With few exceptions (such as SraA, IstR-1, OmrA, RseX and DicF), nearly all known trans-encoded sRNAs annotated in several databases including EcoCyc, RNAMap and BSRD were detected. The expression patterns of some transcripts were further validated by Northern blot analysis.
INSTRUMENT(S): G2565CA DNA microarray scanner (Agilent)
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655
SUBMITTER: Olatz Ruiz-Larrabeiti
PROVIDER: E-MTAB-3329 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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