|
| Status |
Public on Dec 26, 2008 |
| Title |
JF1 mid-log replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
FA19mtrR mutant cells harvested at mid-log phase; 0.6 @600 OD
|
| Organism |
Neisseria gonorrhoeae |
| Characteristics |
FA19mtrR mutant
|
| Growth protocol |
Isolates were grown to mid-log phase in GC broth @ 37°C with supplements and sodium bicarbonate: Shafer, W.M., L. F. Guymon, I. Lind, and P. F. Sparling. 1984. Identification of an envelope mutation (env-10) resulting in increased antibiotic susceptibilit
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by a hot phenol method according to: Ducey, T. F., M. B. Carson, J. Orvis, A. P. Stintzi, and D. W. Dyer. 2005. Identification of the iron-responsive genes of Neisseria gonorrhoeae in microarray analysis in defined medium. J. Bacteriol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to Affymetrix Genechip® Expression Analysis Technical Manual prokaryotic protocol from 10ug of total RNA
|
| |
|
| Hybridization protocol |
Arrays were hybridized using streptavidin phycoerythrin according to Affymetrix protocol ProkGE-WS2v3_450
|
| Scan protocol |
Arrays were scanned using Affymetrix GeneChip Scanner 3000
|
| Description |
none
|
| Data processing |
Data was processed using Genechip Operating Software (GCOS) version 1.4 (Affymetrix, Inc.) GCOS data was then imported into GeneSpring GX 7.3.1 (Agilent Technologies) and normalized per chip by dividing each measurement by the 50th percentile of all the measurements in that sample and per gene by dividing each gene by the median of its measurements across all samples. The cross-gene error model was operating based on replicates. The normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering.
|
| |
|
| Submission date |
Sep 05, 2008 |
| Last update date |
Sep 09, 2008 |
| Contact name |
Lydgia Jackson |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
405 271-1201
|
| Fax |
405 271-1204
|
| Organization name |
University of Oklahoma Health Sciences Center
|
| Department |
Microbiology and Immunology
|
| Lab |
David Dyer
|
| Street address |
975 NE 10th Street
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
| |
|
| Platform ID |
GPL7218 |
| Series (1) |
| GSE12686 |
Expression data from Neisseria gonorrhoeae (FA19) |
|
