E-GEOD-42124 - Steady-state samples of Methanococcus maripaludis MM901 grown on N14 or N15

Status
Released on 16 September 2013, last updated on 2 June 2014
Organism
Methanococcus maripaludis S2
Samples (24)
Array (1)
Protocols (6)
Description
Effects of hydrogen on physiology and regulation of methanogenesis in Methanococcus maripaludis The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). Hydrogen limited condition was 21 mL/min H2. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or nitrogen limiting (3 mM NH4Cl). Culture samples (1.5 mL) were rapidly removed from the vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C. Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.
Experiment type
transcription profiling by array 
Contacts
Sung Ho Yoon <geo@ncbi.nlm.nih.gov>, John A Leigh, June Burn, Min Pan, Nitin S Baliga, Sung-Ho Yoon
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-42124.idf.txt
Sample and data relationshipE-GEOD-42124.sdrf.txt
Raw data (2)E-GEOD-42124.raw.1.zip, E-GEOD-42124.raw.2.zip
Processed data (1)E-GEOD-42124.processed.1.zip
Array designA-GEOD-15063.adf.txt
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