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Status |
Public on Feb 06, 2013 |
Title |
ecfO mutant rep1 |
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.
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|
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Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., using standard protocol as described on their website.
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Scan protocol |
Scanning was performed by NimbleGen Systems Inc., using standard protocol as described on their website.
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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
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|
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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. |
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