|
| Status |
Public on Aug 29, 2023 |
| Title |
BF638R_WT Low iron + oxygen exposure Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Bacteroides fragilis 638R Wild type
|
| Organism |
Bacteroides fragilis 638R |
| Characteristics |
genotype: Wild type
|
| Treatment protocol |
Bacterial cultures were grown to mid-logarithmic phase (O.D. 550 nm of 0.3-0.4), exposed to oxygen for 1h, and submitted to total RNA extract by the hot phenol method.
|
| Growth protocol |
Overnight cultures of Bacteroides fragilis 638R wild type or mutant strains were diluted into minimal defined media supplemented with 5 microgram/ml protoporphyrin IX containing 100 micromolar iron sulfate or 50 micromomolar 2,2-bipyridyl and exposed to atmospheric air (oxygen exposure) for 1 hour.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot phenol method and treatd as described by Sund et al., 2008, Mol. Microbiol. 67:129-142.
|
| Label |
Cy3
|
| Label protocol |
Labeling was peformed by at the FSU Nimblegen Microarray Facility using standard protocols as described previously (Sund et al., 2008, Mol Microbiol. 67:129-142).
|
| |
|
| Hybridization protocol |
Hybridization was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)
|
| Scan protocol |
Scanning was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)
|
| Description |
This sample is of the Bacteroides fragilis 638R fur deletion mutant first of two independent biological replicates from two separate cultures in low iron conditions.
|
| 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. The RMA processed data was averaged and log2 transformed (see *.calls files).
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. The RMA processed data was averaged and log2 transformed (see *.calls files).
|
| |
|
| Submission date |
Aug 24, 2023 |
| Last update date |
Aug 29, 2023 |
| Contact name |
Edson R Rocha |
| E-mail(s) |
[email protected]
|
| Phone |
252-744-9563
|
| Organization name |
East Carolina University Brody School of Medicine
|
| Department |
M
|
| Lab |
Biotech Bldg. Room 130
|
| Street address |
600 Moye Blvd.
|
| City |
Greenville |
| State/province |
NC |
| ZIP/Postal code |
27834 |
| Country |
USA |
| |
|
| Platform ID |
GPL15788 |
| Series (1) |
| GSE241676 |
New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile |
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