|
| Status |
Public on Oct 01, 2006 |
| Title |
Anaerobic pH 5.7 rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli K-12 W3110
|
| Organism |
Escherichia coli |
| Characteristics |
Escherichia coli K-12 W3110
|
| Treatment protocol |
Growth at pH 5.7
|
| Growth protocol |
Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5. Tubes were incubated at37°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2. Five replicate cultures were grown at each pH.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNAprotect (Qiagen) and the RNeasy Kit.
|
| Label |
biotin
|
| Label protocol |
Labeled cDNA was prepared and hybridized to Affymetrix Antisense E. coli arrays by standard procedures.
|
| |
|
| Hybridization protocol |
Affymetrix standard procedures
|
| Description |
Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH during growth without aeration. The experiment was designed for direct comparison with the pH profile under aerobic conditions reported previously (GSE4511). Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5. Tubes were incubated at37°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2. For each of the three pH conditions, RNA was isolated from five independent cultures.
|
| Data processing |
Affymetrix GCOS software
|
| |
|
| Submission date |
Mar 27, 2006 |
| Last update date |
Sep 01, 2006 |
| 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 |
| |
|
| Platform ID |
GPL199 |
| Series (1) |
| GSE4556 |
pH and Anaerobiosis Coregulate Metabolism, Multidrug Transporters, and Envelope Composition in Escherichia coli K-12 |
|
