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| 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
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| 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
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| Overall design |
Samples of genomic DNA and/or cDNA were labeled with Cy3 and Cy5 and cohybridized on six single arrays.
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| Contributor(s) |
Dryselius R, Izutsu K, Iida T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| 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 |
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| Platforms (1) |
| GPL6058 |
Vibrio parahaemolyticus RIMD2210633 5k microarray |
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| Samples (8)
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| 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 |
| GSM252057 |
V. parahaemolyticus cDNA 3%LB at 37°C vs gDNA non-replicating |
| GSM252058 |
V. parahaemolyticus cDNA 3%LB at 37°C vs cDNA 3%M90.4%glucose |
| GSM252059 |
V. parahaemolyticus cDNA 3%LB early logarithmic growth at 37°C vs cDNA 3%LB late logarithmic/early stationary growth |
| GSM281581 |
V. parahaemolyticus cDNA 3%LB at 20°C vs gDNA non-replicating |
| GSM281582 |
V. parahaemolyticus cDNA 3%M90.4%glucose vs gDNA non-replicating |
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| Relations |
| BioProject |
PRJNA103985 |
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