|
| Status |
Public on Aug 03, 2011 |
| Title |
E. coli control at time=60 min, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
E. coli T=60 min, no treatment, rep 1
|
| Organism |
Escherichia coli |
| Characteristics |
strain: D31
|
| Treatment protocol |
At OD600 = 0.4, the culture of E.coli was split into 9 equal flasks containing prewarmed LB media: three containing 1X volume of LB media with no antimicrobial, three containing 1X volume of LB media + 17.5 µg/mL PMX 10070 (for a final concentration of 8.75 µg/mL PMX 10070) and three containing 1X volume of LB media + 0.78 µg/mL of Polymyxin B sulfate (for a final concentration of 0.39 µg/mL Polymyxin B sulfate)
|
| Growth protocol |
Cultures of E.coli were grown from dilutions of overnight cultures in LB media at 37C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 mL of culture was harvested from each sample at indicated times and Qiagen Rneasy mini kit isolation of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA
|
| |
|
| Hybridization protocol |
10 ug of cRNA were hybridized for 16 hr at 45C on E. coli Genome 2.0 Array. The microarrays were then washed and stained.
|
| Scan protocol |
Genechips were scanned with a GCS3000 laser scanner.
|
| Description |
DeGrado2_ (1290) GC10 E. coli_2
Gene expression data from E. coli in late logarithmic growth
|
| Data processing |
Data were GC-RMA normalized and processed using SAM (significance analysis of Microarrays)
|
| |
|
| Submission date |
Aug 02, 2011 |
| Last update date |
Aug 03, 2011 |
| Contact name |
Bruk Mensa |
| E-mail(s) |
[email protected]
|
| Phone |
215-898-3495
|
| Organization name |
University of Pennsylvania, School of Medicine
|
| Department |
Biochemistry and Biophysics
|
| Lab |
DeGrado Lab
|
| Street address |
1010 Stellar Chance Building, 422 Curie Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE31140 |
E.coli response to Antimicrobial Arylamides |
|
