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E-GEOD-38259 - Gene expression analysis of Photobacterium profundum DB110 and TW30 toxR mutant strain at 0.1 MPa and 28 MPa

Released on 22 December 2012, last updated on 7 January 2013
Photobacterium profundum
Samples (4)
Protocols (4)
Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of wild type (DB110) and toxR (TW30) mutant strains of the deep-sea bacterium Photobacterium profundum. ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae and able to regulate numerous genes involved in virulence. In P. profundum the abundance and activity of the same protein is influenced by hydrostatic pressure and is able to regulate genes in a pressure-dependent manner. To better characterize the ToxR regulon, we have compared the genes differentially expressed in response to pressure changes with those whose expression is altered between wild type and toxR mutant strains. Four samples were analyzed: DB110 strain grown at 0.1 MPa, DB110 strain grown at 28 MPa, TW30 strain grown at 0.1 MPa, TW30 strain grown at 28 MPa. Two independent coltures (replicates) were grown for each sample, RNA was extracted from each replicate and RNAs from the two replicates were pooled together to reduce biological variability. No replicates were included in experimental design.
Experiment type
RNA-seq of coding RNA 
Douglas Bartlett, Giorgio Valle, Stefano Campanaro
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-38259.idf.txt
Sample and data relationshipE-GEOD-38259.sdrf.txt
Processed data (1)