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Series GSE4778 Query DataSets for GSE4778
Status Public on Feb 20, 2008
Title Acid-Shifted Time Course of Gene Expression Profiles of Aerobically Grown Escherichia coli K-12
Platform organism Escherichia coli K-12
Sample organism Escherichia coli
Experiment type Expression profiling by array
Summary The effect of an extracellular acid shift on gene expression profiles of Escherichia coli K-12 W3110 was observed using Affymetrix E. coli arrays. In order to maximize aeration and maintain logarithmic growth, the overnight culture (LBK broth medium) was diluted 500-fold into a 250-ml baffled flask containing 55 ml of 20mM HOMOPIPES buffered medium (pH 7.6). Cultures were grown to OD600=0.2. A shift to acid external pH was conducted by rapid addition of 840 µl 1M HCl, which lowered the pH of the medium to pH 5.5. For each of five biological replicates, 10-ml samples were taken at times 0, 1, 5, and 10 min post addition of HCl. Each sample was added to 1 ml 10% phenol-ethanol stop solution in <5 sec. For each sample, cDNA synthesized from total RNA was hybridized onto Affymetrix E. coli arrays. Model-based gene expression intensities were determined using GCOS software. Gene-by-gene temporal differential expression was analyzed as a mixed-effects model using polynomial time functions as fixed effects and flask variation as a random effect.
Keywords: Time Course
 
Overall design Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of time versus change in external pH. Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 20 mM HOMOPIPES at 7.6. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 225 rpm, incubated at 37°C to an optical density at 600 nm of 0.2. External pH was lowered to pH 5.5 by adding 840 µl of 1M HCl to 40 mls of culture within 5 seconds. Four samples were taken from each of five replicate cultures, corresponding to time 0 (before HCl addition),1, 5, and 10 min post HCl addition.
 
Contributor(s) Kannan G, Wilks JC, BonDurant SS, Jones BD, Slonczewski JL
Citation(s) 18302792
Submission date May 05, 2006
Last update date Mar 16, 2012
Contact name Joan Lyn Slonczewski
E-mail(s) slonczewski@kenyon.edu
Phone 740-427-5397
URL http://biology.kenyon.edu/slonc/slonc.htm
Organization name Kenyon College
Department Biology Dept
Street address 202 N. College Rd
City Gambier
State/province OH
ZIP/Postal code 43022
Country USA
 
Platforms (1)
GPL199 [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array
Samples (20)
GSM105392 Acid shift time 0 rep 1
GSM105393 Acid shift time 0 rep 2
GSM105394 Acid shift time 0 rep 3
Relations
BioProject PRJNA95551

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Supplementary file Size Download File type/resource
GSE4778_RAW.tar 26.8 Mb (http)(custom) TAR (of CEL)
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