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Series GSE9968 Query DataSets for GSE9968
Status Public on Nov 20, 2008
Title Examination of growth mode dependent replication dynamics and expression levels for Vibrio parahaemolyticus RIMD2210633.
Platform organism Vibrio parahaemolyticus RIMD 2210633
Sample organisms Vibrio parahaemolyticus; Vibrio parahaemolyticus RIMD 2210633
Experiment type Expression profiling by array
Genome variation profiling by array
Summary Replication of bacterial chromosomes increases the copy numbers of genes located near the origin of replication relative to genes located near the terminus. Such differential gene dosage is variable and depends on several factors including replication rate, generation time and chromosome size. For vibrios, a diverse family of fast growing marine living gammaproteobacteria, gene dosage effects may be particularly important as they harbour their genome within two differently sized chromosomes. In this series of experiments, gene dosage at the genomic level and its influence on the expression level has been examined in V. parahaemolyticus. For the genomic analyses, gene copy numbers for bacteria in mid-logarithmic phase grown in rich media (Luria-Bertani containing 3% (w/v) NaCl) at two temperatures (37°C or 20°C) or in minimal media (M9 containing 3% (w/v) NaCl and 0.4% (w/v) glucose) were compared against gene copy numbers for non-replicating cells. For expression analyses, cDNA derived from bacteria in mid-logarithmic phase grown in rich broth at two temperatures (37°C or 20°C) or in minimal media were compared against gDNA from non-replicating cells. Also, cDNA derived from early (OD600=0.2) or mid-logarithmic phase bacteria (OD600=0.5) in rich broth at 37°C, were compared against cDNA derived from mid-logarithmic cells in minimal media (OD600=0.5) or cDNA from early stationary phase rich broth cells (OD600=3.0).
Keywords: Comparative genomic and/or cDNA hybridization
Overall design Samples of genomic DNA and/or cDNA were labeled with Cy3 and Cy5 and cohybridized on six single arrays.
Contributor(s) Dryselius R, Izutsu K, Iida T
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Submission date Dec 19, 2007
Last update date Mar 17, 2012
Contact name Kaori Izutsu
Organization name Osaka University
Department Research Institute for Microbial Diseases
Lab Laboratory of Genomic Research on Pathogenic Bacteria
Street address 1-1 Yamadaoka
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
Platforms (1)
GPL6058 Vibrio parahaemolyticus RIMD2210633 5k microarray
Samples (8)
GSM252054 V. parahaemolyticus gDNA 3%LB at 37°C vs gDNA non-replicating
GSM252055 V. parahaemolyticus gDNA 3%LB at 20°C vs gDNA non-replicating
GSM252056 V. parahaemolyticus gDNA 3%M90.4%glucose at 37°C vs gDNA non-replicating
BioProject PRJNA103985

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
GSE9968_RAW.tar 1.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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