|
| Status |
Public on Mar 23, 2006 |
| Title |
Aerobic pH 7.0 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli K-12 W3110
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
Escherichia coli K-12 W3110
|
| Treatment protocol |
Growth at pH 7.0
|
| Growth protocol |
Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7. Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3. 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
|
| Scan protocol |
Affymetrix standard procedures
|
| Description |
Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7. Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3. For each of the three pH conditions, RNA was isolated from five independent cultures.
|
| Data processing |
Affymetrix GCOS software
|
| |
|
| Submission date |
Mar 21, 2006 |
| Last update date |
Jan 24, 2007 |
| 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) |
| GSE4511 |
pH Regulates Genes for Flagellar Motility, Catabolism, and Oxidative Stress in Escherichia coli K-12 |
|
