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Sample GSM7733637 Query DataSets for GSM7733637
Status Public on Aug 29, 2023
Title BF638R_WT High iron anaerobic control 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 wild type second of two independent biological replicates from two separate cultures in high 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 11.61859
BF638000000000002 4.93333
BF638000000000003 3.11172
BF638000000000004 4.25662
BF638000000000005 6.68515
BF638000000000006 9.12498
BF638000000000007 6.97615
BF638000000000008 5.21772
BF638000000000009 6.19853
BF638000000000010 5.59391
BF638000000000011 5.29629
BF638000000000012 9.35891
BF638000000000013 5.89292
BF638000000000014 11.12118
BF638000000000015 10.49508
BF638000000000016 11.02734
BF638000000000017 12.78182
BF638000000000018 14.26596
BF638000000000019 12.00035
BF638000000000020 11.17117

Total number of rows: 4341

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM7733637_GEO_Rocha_Sample2_wt2_high_iron_anaerobic_control.txt.txt.gz 28.9 Kb (ftp)(http) TXT
GSM7733637_Rocha_S2_BF638R_Wt_High_iron_anaerobic_control_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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