|
| Status |
Public on Feb 06, 2013 |
| Title |
ecfO mutant rep2 |
| Sample type |
RNA |
| |
|
| Source name |
ecfO null_empty vector
|
| Organism |
Bacteroides fragilis 638R |
| Characteristics |
genotype/variation: ecfO null mutant with empty vector control
|
| Growth protocol |
Overnight cultures of the vector control or IPTG inducible strain were diluted 1/50 into complex media. IPTG was added and cultures were grown under anaerobic conditions at 37C
to mid-logarithmic phase at A550 of 0.3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., using standard protocol as described on their website.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., using standard protocol as described on their website.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., using standard protocol as described on their website.
|
| Description |
ecfO mutant with empty vector control for IPTG induced expression of ecfO experiment
|
| Data processing |
Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site.
Two of the .pair files (ecfO_bio_rep3.pair and reo+pEcfO_bio_rep4.pair) are missing some chip quality control/tracking information resulting less data rows that other raw data files
|
| |
|
| Submission date |
Jul 10, 2012 |
| Last update date |
Feb 06, 2013 |
| Contact name |
Charles Jeffrey Smith |
| E-mail(s) |
[email protected]
|
| Phone |
252-744-2700
|
| Fax |
252-744-3104
|
| Organization name |
East Carolina University
|
| Department |
Microbiology & Immunology
|
| Street address |
600 Moye Blvd.
|
| City |
Greenville |
| State/province |
NC |
| ZIP/Postal code |
27834 |
| Country |
USA |
| |
|
| Platform ID |
GPL15788 |
| Series (1) |
| GSE39231 |
Role of the Bacteroides fragilis EcfO regulon during oxidative stress. |
|
