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Sample GSM7733643 Query DataSets for GSM7733643
Status Public on Aug 29, 2023
Title BF638R_WT Low iron + oxygen exposure Rep2
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 second 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

Data table header descriptions
ID_REF
VALUE quantile

Data table
ID_REF VALUE
BF638000000000001 11.47365
BF638000000000002 4.7807
BF638000000000003 3.73864
BF638000000000004 4.74378
BF638000000000005 6.6318
BF638000000000006 8.98907
BF638000000000007 7.36729
BF638000000000008 5.6724
BF638000000000009 5.84155
BF638000000000010 5.15066
BF638000000000011 4.11765
BF638000000000012 9.93021
BF638000000000013 7.31037
BF638000000000014 11.591
BF638000000000015 11.25203
BF638000000000016 11.07638
BF638000000000017 9.51404
BF638000000000018 12.13468
BF638000000000019 7.29137
BF638000000000020 12.70155

Total number of rows: 4341

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM7733643_GEO_Rocha_Sample8_Wt2_Low_iron_+_oxygen_exposure.txt.txt.gz 29.1 Kb (ftp)(http) TXT
GSM7733643_Rocha_S8_BF638R_Wt_Low_iron_oxygen_exposure_Rep2_532_norm_RMA.pair.gz 5.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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