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| Status |
Public on Jul 29, 2008 |
| Title |
Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in R. sphaeroides |
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Experiment type |
Expression profiling by array
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| Summary |
we performed time series microarray analyses to investigate transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration. Published on J. Bacteriol., 190 (1), 286-299, 2008.
Major changes in gene expression profiles occurred in the initial 15 min after the shift from anaerobic-light to aerobic-dark conditions, with changes continuing to occur up to 4 hours postshift. Those genes whose expression levels changed significantly during the time series were grouped into three major classes by clustering analysis. Class I contained genes, such as that for the aa3 cytochrome oxidase, whose expression levels increased after the shift. Class II contained genes, such as those for the photosynthetic apparatus and Calvin cycle enzymes, whose expression levels decreased after the shift. Class III contained genes whose expression levels temporarily increased during the time series.
Keywords: time course
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| Overall design |
R. sphaeroides 2.4.1 was grown in 800 ml of medium in 1-liter glass bottles under anaerobic photosynthesis conditions. When the optical density at 600 nm (OD600) reached approximately 0.2 to 0.3, the light was turned off and the composition of the gas mixture was abruptly changed for aerobic growth conditions. RNA was isolated from a 50-ml aliquot of the culture prior to the shift to aerobic conditions (0 min) and at 15 min, 30 min, 1 h, 2 h, and 4 h after the shift. The final OD600 at 4 h was approximately 0.3 to 0.4, representing not quite a culture doubling. The experiment was performed in quadruplicate independent cultures.
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| Contributor(s) |
Arai H, Roh JH, Kaplan S |
| Citation(s) |
17965166 |
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| Submission date |
Jul 28, 2008 |
| Last update date |
Apr 26, 2014 |
| Contact name |
Jung Hyeob Roh |
| E-mail(s) |
jung.h.roh@uth.tmc.edu, junghyeob@gmail.com
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| Phone |
713-500-5437
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| Organization name |
The University of Texas
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| Department |
Microbiology & Molecular Genetics
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| Street address |
6431 Fannin St.
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL162 |
[uwyRhodo1a] Rhodobacter sphaeroides 2.4.1 GeneChip |
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| Samples (24)
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| GSM308087 |
1hr after shift, biological rep1 |
| GSM308088 |
2hr after shift, biological rep1 |
| GSM308089 |
4hr after shift, biological rep1 |
| GSM308090 |
before shift, biological rep2 |
| GSM308091 |
15min after shift, biological rep2 |
| GSM308092 |
30min after shift, biological rep2 |
| GSM308093 |
1hr after shift, biological rep2 |
| GSM308094 |
2hr after shift, biological rep2 |
| GSM308095 |
4hr after shift, biological rep2 |
| GSM308096 |
before shift, biological rep3 |
| GSM308097 |
15min after shift, biological rep3 |
| GSM308098 |
30min after shift, biological rep3 |
| GSM308099 |
1hr after shift, biological rep3 |
| GSM308100 |
2hr after shift, biological rep3 |
| GSM308101 |
4hr after shift, biological rep3 |
| GSM308102 |
before shift, biological rep4 |
| GSM308103 |
15min after shift, biological rep4 |
| GSM308104 |
30min after shift, biological rep4 |
| GSM308105 |
1hr after shift, biological rep4 |
| GSM308106 |
2hr after shift, biological rep4 |
| GSM308107 |
4hr after shift, biological rep4 |
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| Relations |
| BioProject |
PRJNA113653 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12269_RAW.tar |
18.1 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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