E-SMDB-3833 - Transcription profiling of Vibrio cholerae wild type, hapR and rpoS deletions in mid-exponential or stationary phase concluding that rpoS controls the Vibrio cholerae mucosal escape response

Status
Released on 6 November 2006, last updated on 27 March 2012
Organism
Vibrio cholerae
Samples (0)
Array (1)
Protocols (4)
Description
For expression analysis of wild-type V. cholerae, hapR, and rpoS deletion mutants in mid-exponential or stationary phase, the strains were grown to either OD600 of 0.3 or for 11 h in LB media at 37 0C, and bacteria from 2-ml culture were quickly pelleted, resuspended in Trizol reagent (GIBCO/BRL, San Diego, California, United States), and frozen on dry ice. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. At least four microarray experiments were performed for each of two biological replicates for the tested strains. Gene expression of V. cholerae, rpoS, and hapR deletion mutants in stationary phase LB cultures was analyzed and compared to the wild-type parent under identical conditions. Gene expression of the wild-type parent during stationary phase after 11 h growth in LB was analyzed using RNA from an exponentially growing culture as a reference.
Experiment types
transcription profiling by array, strain or line
Contacts
Citation
RpoS Controls the Vibrio cholerae Mucosal Escape Response. Nielsen AT, Dolganov NA, Otto G, Miller MC, Wu CY, Schoolnik GK. PLoS Pathog 2(10) (2006), PMID:17054394
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-SMDB-3833.idf.txt
Sample and data relationshipE-SMDB-3833.sdrf.txt
Raw data (1)E-SMDB-3833.raw.1.zip
Processed data (1)E-SMDB-3833.processed.1.zip
Array designA-SMDB-356.adf.txt