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Series GSE8544 Query DataSets for GSE8544
Status Public on Oct 11, 2007
Title Effects of Oxygen on Virulence Traits of Streptococcus mutans
Organism Streptococcus mutans
Experiment type Expression profiling by array
Summary To gain further insights into the molecular basis of the effects of oxygen on biofilm formation by S. mutans (Ahn and Burne, 2007), we used DNA microarrays to analyze gene expression profiles of cells cultured under aerobic or anaerobic conditions.
Keywords: Oxygen, Biofilm, Caries, Microarray
Overall design For aerobic growth, an overnight culture of S. mutans UA159 was diluted 1:50 into a 250-ml conical flask containing 50 ml of brain heart infusion (BHI, Difco) and cultures were grown on a rotary shaker (150 rpm) at 37°C until the absorbance at 600 nm reached 0.4 (mid-exponential phase). For anaerobic growth, cultures were similarly diluted and incubated without agitation in a BBL GasPak Plus anaerobic system (BD, Franklin Lakes, NJ) to the same optical density.

Total RNA was isolated from 10 ml of exponential phase (O.D.600 = 0.4) cultures, as described previously. All RNA samples were DNase I-treated and purified using the RNeasy mini kit (Qiagen). RNA concentration was estimated spectrophotometrically in triplicate. Reverse transcription (RT) and microarray reactions were performed with 5.0 μg of total bacterial RNA, as described elsewhere. S. mutans UA159 microarrays were provided by The Institute for Genomic Research (TIGR), and each slide contained four copies of 1960 corresponding to ORFs in the genome. For each microarray slide, a separate RNA preparation from a separate culture was utilized, so a total of 8 slides (4 for each condition) were used in this study. Hybridizations were performed in a Maui hybridization chamber (BioMicro Systems, Salt Lake City, UT). Additional details regarding array protocols are available at

After the slides were scanned, the resulting images were analyzed by TIGR 23
Spotfinder software ( and further normalized using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis using TIGR microarray data analysis system (MIDAS; Statistical analysis was carried out using BRB array tools ( with a cutoff P value of 0.001.

Contributor(s) Ahn S, Wen ZT, Burne RA
Citation(s) 17921307
Submission date Jul 20, 2007
Last update date Aug 10, 2016
Contact name Robert A Burne
Phone 352-846-2520
Organization name University of Florida
Department Oral Biology
Lab Burne Lab
Street address 1600 SW Archer Rd. BOX 100424
City Gainesville
State/province FL
ZIP/Postal code 32610-0424
Country USA
Platforms (1)
GPL4340 JCVI PFGRC Streptococcus mutans 10K v2.1 array designed primarily based on strain UA159 [FULL_FEATURE_LAYOUT]
Samples (8)
GSM236979 SmutansUA159_anaerobic_rep1
GSM236980 SmutansUA159_anaerobic_rep2
GSM236981 SmutansUA159_anaerobic_rep3
BioProject PRJNA101687

ClassComparison_0.001_fold_difference header descriptions
Unique id
Parametric p-value
Geom mean of ratios in class 1 : C
Geom mean of ratios in class 2 : O2
Functional category

Data table
Unique id Parametric p-value Geom mean of ratios in class 1 : C Geom mean of ratios in class 2 : O2 Value Functional category Description
SMU.423 < 1e-07 0.794 33.324 41.9697733 Unassigned hypothetical protein
SMU.1912c 0.0000001 0.731 24.763 33.875513 Hypothetical hypothetical protein
SMU.1904c < 1e-07 0.861 28.906 33.57259001 Hypothetical hypothetical protein
SMU.1913c < 1e-07 0.874 28.8 32.95194508 Hypothetical putative immunity protein, BLpL-like
SMU.1903c 0.0000006 0.894 26.676 29.83892617 Hypothetical hypothetical protein
SMU.1425 < 1e-07 0.92 27.414 29.79782609 Protein fate putative Clp proteinase, ATP-binding subunit ClpB
SMU.150 < 1e-07 0.864 24.874 28.78935185 Hypothetical hypothetical protein
SMU.151 < 1e-07 0.672 18.824 28.01190476 Hypothetical hypothetical protein
SMU.1905c < 1e-07 0.604 16.084 26.62913907 Hypothetical putative bacteriocin secretion protein
SMU.152 < 1e-07 0.867 21.052 24.28143022 Hypothetical hypothetical protein
SMU.1906c < 1e-07 0.858 20.634 24.04895105 Hypothetical hypothetical protein
SMU.1914c 0.0000002 0.882 15.742 17.84807256 Hypothetical hypothetical protein
SMU.1909c 0.0003066 0.877 12.564 14.32611174 Hypothetical hypothetical protein
SMU.148 0.0000001 1.155 16.415 14.21212121 Energy metabolism putative alcohol-acetaldehyde dehydrogenase
SMU.1424 0.0000364 0.36 5.035 13.98611111 Energy metabolism putative dihydrolipoamide dehydrogenase
SMU.575c 0.0000492 0.853 9.943 11.65650645 Unassigned putative membrane protein
SMU.2057c 0.0000005 1.149 10.934 9.516100957 Cellular processes putative cadmium-transporting ATPase P-type ATPase
SMU.78 0.0000002 1.132 9.763 8.624558304 Energy metabolism fructan hydrolase exo-beta-D-fructosidase; fructanase, FruA
SMU.1539 0.0000007 0.891 7.326 8.222222222 Energy metabolism putative 1,4-alpha-glucan branching enzyme
SMU.79 0.0000032 0.817 6.431 7.871481028 Energy metabolism fructan hydrolase exo-beta-D-fructosidase; FruB

Total number of rows: 106

Table truncated, full table size 10 Kbytes.

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE8544_RAW.tar 2.3 Mb (http)(custom) TAR (of MEV)
Processed data included within Sample table

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