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| Status |
Public on Dec 31, 2008 |
| Title |
mRNA expression in TTHA0118 deletion mutant of Thermus thermophilus HB8 strain grown on minimum essential medium |
| Organism |
Thermus thermophilus HB8 |
| Experiment type |
Expression profiling by array
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| Summary |
We compared the expression profile of TTHA0118 deletion mutant strain of Thermus thermophils HB8 with that of wild-type. The mutant strain grown in minimum essential medium (CS medium) exhibited growth retardation. In early log phase, 29 genes were suppressed and 25 genes were activated for the mutant strain. The suppressed genes included genes of electron transport, and cell growth and division. The activated genes included genes of stress response. We suggested that these transcriptional alterations in the mutant cell were induced by the pAp accumulation and mononucleotides starvation. Keywords: cell type comparison
Keywords: cell type comparison
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| Overall design |
Wild-type and the mutant strains were precultured in rich medium (TT medium) for two times at 70 oC and then subcultured to minimum essential medium (CS medium). These cells were harvested at 7 × 10^8 cells/ml. Total RNA were extracted from each strain and used for the cDNA synthesis. For the biological replication, above experiments were performed four times independently. The cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer's instructions. The 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401 GeneChip (Affymetrix). The Probe Array was scanned with a GeneArray Scanner (Affymetrix), and then, the image data was scaled to the target intensity by one-step Tukey's biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix). The data analysis was performed by using GeneSpring GX (Agilent Tech.). The genes which had detection call of 'presence' more than 4 times from 8 samples were used for following analysis. The normalized intensities for the mutant strains were calculated by using the intensities for wild-type strains of each data set, and then, the average of these intensities were used. The genes which produced P value < 0.05 in the Student's t-test were extracted. Among them, the genes whose expression level was different more than 2 fold between two strains were considered as significant.
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| Contributor(s) |
Wakamatsu T, Nakagawa N, Masui R, Kuramitsu S |
| Citation missing |
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| Submission date |
Aug 27, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Taisuke Wakamatsu |
| E-mail(s) |
taisuke@bio.sci.osaka-u.ac.jp
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| Phone |
+81-6-6850-5434
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| Fax |
+81-6-6850-5442
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| URL |
http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/kuramitu/
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| Organization name |
Osaka University
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| Department |
Department of Biology
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| Lab |
Structural and Functional Analyses on Biomolecules
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| Street address |
Machikaneyama 1-1
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| City |
Toyonaka |
| State/province |
Osaka |
| ZIP/Postal code |
560-0043 |
| Country |
Japan |
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| Platforms (1) |
| GPL4902 |
Riken Thermus thermophilus HB8 4K mRNA array |
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| Samples (8)
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| GSM315680 |
wild-type strain_CS medium_4 |
| GSM315681 |
TTHA0118 deletion mutant strain_CS medium_1 |
| GSM315682 |
TTHA0118 deletion mutant strain_CS medium_2 |
| GSM315683 |
TTHA0118 deletion mutant strain_CS medium_3 |
| GSM315684 |
TTHA0118 deletion mutant strain_CS medium_4 |
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| Relations |
| BioProject |
PRJNA112839 |
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