|
| Status |
Public on Jul 26, 2007 |
| Title |
E. coli dpp 100 GSNO Sample2 TechRep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
E. coli dpp- mid-log aerobic 37C in MOPS glucose
|
| Organism |
Escherichia coli |
| Characteristics |
BW25113/dppABCDF-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted by hot phenol chloroform followed by Qiagen RNA Midi column.
|
| Label |
Cy3
|
| Label protocol |
Samples were directly labeled by direct incorporation of labeled dCTP.
|
| |
|
| Channel 2 |
| Source name |
E. coli dpp- 5 minutes after the addition of 100uM GSNO
|
| Organism |
Escherichia coli |
| Characteristics |
BW25113/dppABCDF-
|
| Treatment protocol |
Treated with 100 micromolar GSNO for 5 minutes prior to harvesting
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted by hot phenol chloroform followed by Qiagen RNA Midi column.
|
| Label |
Cy5
|
| Label protocol |
Samples were directly labeled by direct incorporation of labeled dCTP.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized as specified in the Corning UltraGAPS manual. Slides were blocked and washed as specified in the Corning UltraGAPS manual.
|
| Scan protocol |
Slides were scanned immediately after washing with a Virtek/BioRad scanner.
|
| Description |
Cells were grown in MOPS media/0.5% glucose and aerobic conditions.
|
| Data processing |
Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files. The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)
|
| |
|
| Submission date |
Jul 19, 2007 |
| Last update date |
Jul 25, 2007 |
| Contact name |
Laura R Jarboe |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Los Angeles
|
| Department |
Chemical and Biomolecular Engineering
|
| Street address |
420 Westwood Pl
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL5113 |
| Series (1) |
| GSE8540 |
Identification of GSNO response network in E. coli |
|
