|
| Status |
Public on Aug 15, 2007 |
| Title |
wt 360 minutes growth rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli MG1655 wt grown 360 minutes
|
| Organism |
Escherichia coli |
| Characteristics |
wildtype Escherichia coli
360 minutes growth in LB
|
| Treatment protocol |
Cells were grown in LB at 37 degrees celsius with shaking for 360 minutes
|
| Growth protocol |
Saturated E. coli cultures were diluted in LB toan OD.of 0.05 OD600, grown at 37 degrees Celsius
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MasterPure RNA purification Kit per manufacturers protocol
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip E.coli antisense. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from MG1655 wildtype after 360 minutes of growth in LB medium
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Data from this sample were collected using Affy Ecoli anti-sense chip (2001; platform ID GPL4940), but because the analysis software failed to recognize the correct platform, we reformatted the data to match the newer (and mostly equivalent) platform GPL199 (Affy Ecoli anti-sense chip version 2, 2002). Because, however, not all of the probes on the new platform were present on the old platform, data for some probes were unavailable and labeled in the 'remapped' dataset as 'NULL' to indicate they were missing. While the following data are therefore formatted using ID_REFs that match GPL199, the CEL file contains the raw data (not 'remapped') and thus corresponds to the actual array used (GPL4940, Ecoli antisense chip, 2001).
|
| |
|
| Submission date |
Mar 27, 2007 |
| Last update date |
Mar 29, 2007 |
| Contact name |
Robert Osuna |
| E-mail(s) |
osuna@albany.edu
|
| Phone |
518-591-8827
|
| Fax |
518-442-4767
|
| Organization name |
University at Albany
|
| Department |
Biology
|
| Lab |
Dr. Osuna
|
| Street address |
1400 Washington Avenue
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12222 |
| Country |
USA |
| |
|
| Platform ID |
GPL199 |
| Series (2) |
| GSE7380 |
WT (Fis+) strain |
| GSE7398 |
Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains |
|
