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Series GSE40811 Query DataSets for GSE40811
Status Public on Aug 21, 2013
Title Transcriptional profiling of Escherichia coli after addition of CORM-3 and iCORM-3 to aerobically and anaerobically growing cells
Organism Escherichia coli
Experiment type Expression profiling by array
Summary Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 2 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CORM-3 or iCORM-3 was added to the chemostat culture at a final concentration of 40 uM.
Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to (i)CORM-3 for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
 
Overall design Time course experiment with samples taken immediately prior to or 2.5, 5, 10, 20, 40 or 80 minutes after addition of either 40uM CORM-3 or iCORM-3 under either 0 or 100 % perceived aerobiosis. 2 biological repeats were performed for each condition with 2 technical (dye swap) repeats per biological repeat.
 
Contributor(s) McLean S, Poole RK
Citation(s) 23472713
Submission date Sep 12, 2012
Last update date Nov 21, 2013
Contact name Robert Poole
E-mail(s) R.poole@shef.ac.uk
Phone 01142224447
Organization name University of Sheffield
Department Molecular Biology & Biotechnology
Lab F13
Street address Firth Court, Western Bank
City Sheffield
State/province South Yorkshire
ZIP/Postal code S10 2TN
Country United Kingdom
 
Platforms (1)
GPL16048 Agilent-029412 E. coli K-12 MG1655 Summer 2010_Updated annotation
Samples (96)
GSM1002270 Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 2.5
GSM1002271 Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 5
GSM1002272 Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 10
Relations
BioProject PRJNA175034

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40811_RAW.tar 148.6 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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