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Status |
Public on Aug 29, 2023 |
Title |
BF638R_fur_mut Low iron + oxygen exposure Rep1 |
Sample type |
RNA |
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Source name |
Bacteroides fragilis 638R fur deletion mutant
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Organism |
Bacteroides fragilis 638R |
Characteristics |
genotype: fur deletion mutant
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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.
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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.
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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.
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Label |
Cy3
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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).
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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)
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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)
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Description |
This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in high heme conditions.
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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).
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Submission date |
Aug 24, 2023 |
Last update date |
Aug 29, 2023 |
Contact name |
Edson R Rocha |
E-mail(s) |
[email protected]
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Phone |
252-744-9563
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Organization name |
East Carolina University Brody School of Medicine
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Department |
M
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Lab |
Biotech Bldg. Room 130
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Street address |
600 Moye Blvd.
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City |
Greenville |
State/province |
NC |
ZIP/Postal code |
27834 |
Country |
USA |
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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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