|
| Status |
Public on Feb 20, 2008 |
| Title |
Acid shift time 0 rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli K-12 W3110
|
| Organism |
Escherichia coli |
| Characteristics |
Escherichia coli K-12 W3110
|
| Treatment protocol |
Growth at pH 7.6
|
| Growth protocol |
E. coli K-12 strain W3110 was diluted 500- fold in potassium-modified Luria-Bertani medium (LBK) buffered with 20 mM HOMOPIPES at pH 7.6. The cultures were rotated at 225 rpm at 37ºC. Cultures were grown to an optical density at 600 nm of 0.2. External pH was lowered to 5.5 with 1 M HCl. 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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using 10% saturated phenol-ethanol solution 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 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.
|
| Data processing |
Affymetrix GCOS software
|
| |
|
| Submission date |
Apr 14, 2006 |
| Last update date |
Feb 19, 2008 |
| 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) |
| GSE4778 |
Acid-Shifted Time Course of Gene Expression Profiles of Aerobically Grown Escherichia coli K-12 |
|
