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E-GEOD-20379 - S. oneidensis MR-1 with electrode, Fe(III)citrate and oxygen as electron acceptor

Status
Released on 1 February 2011, last updated on 27 January 2013
Organism
Shewanella oneidensis MR-1
Samples (9)
Array (1)
Protocols (13)
Description
S. oneidensis MR-1 was grown with different electron acceptors: an electrode at 0.4 V vs. SHE, 50 mM Fe(III)citrate, and oxygen. The gene expression pattern for each experiment was analyzed and the differences in gene expression for the different experimental conditions were compared. For two samples S. oneidensis was grown with a graphite anode electrode (at 0.4 V. vs. SHE) as the only electron acceptor - one sample was directly fed with 20 mM lactate, one sample was fed with lactate produced during fermentation of glucose by Lactococcus lactis. Four samples were grown anaerobically with 50 mM Fe(III)citrate as the only electron acceptor, and 20 mM lactate for 20 h. Three samples were grown aerobically with 20 mM lactate for 20 h. The same modified M4 medium was used for all samples. For RNA extraction, the biofilm was scraped off the frozen (-80°C) carbon electrode with a sterile razor blade. Biofilm-carbon sludge was combined with 7 mL ice-cold phosphate buffer saline (PBS), vortexed, sonicated at 7 W for 30 s on ice (3 repetitions), and centrifuged. For the liquid cultures, 2 mL of each culture were combined with 2 mL RNA protect, vortexed, and centrifuged at 5,500g for 10 min. The pellets were resuspended in NAES buffer (50 mM sodium acetate buffer, 10 mM EDTA and 1 % SDS at pH 5). RNA was isolated with a phenol:chloroform extraction protocol.
Experiment type
transcription profiling by array 
Contacts
Miriam Rosenbaum <mr625@cornell.edu>, Haim Y Bar, Lars Angenent, Qasim Beg
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-20379.idf.txt
Sample and data relationshipE-GEOD-20379.sdrf.txt
Raw data (1)E-GEOD-20379.raw.1.zip
Processed data (1)E-GEOD-20379.processed.1.zip
Array designA-GEOD-8434.adf.txt
Links