|
| Status |
Public on Mar 06, 2018 |
| Title |
PCC6803_Light_30_rep3_for check repeatability |
| Sample type |
RNA |
| |
|
| Source name |
PCC6803, Light30, replicate 3, for check repeatability
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
light intensity: 30
|
| Treatment protocol |
PCC 6803 was cultivated in tubular photo-bioreactor and harvested at OD730 ≈ 0.6, corresponding to the mid exponential phase. The broth was mixed with an equal volume of 10% (w/v) phenol in ethanol, and cells were collected by centrifugation. The cells were immediately frozen in liquid nitrogen and stored at -80°C.
|
| Growth protocol |
The glucose-tolerant wild type strain of Synechocystis sp. PCC 6803 was cultivated in modified BG-11 medium. Cells were cultivated in a 1000 ml tubular photo-bioreactor with 400 ml of modified BG11 medium at 34°C with an agitation rate of 200 rpm, bubbled with 1.0 vvm of air containing 2.5% (v/v) CO2. The light source was a custom LED (CCS, ISL-R100X100-RRRB), with the light intensity of the red and blue lights being 5: 1, and the total light intensity was regulated to adjust the measurements in the center of culture tank to a predetermined value.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ambion Ribopure yeast kit (Life Technologies Co., Carlsbad, CA)
|
| Label |
Cy3
|
| Label protocol |
Fairplay III microarray labeling kit (Agilent Technologies)
|
| |
|
| Hybridization protocol |
Gene Expression Hybridization kit (Agilent Technologies)
|
| Scan protocol |
Agilent G2565CA microarray scanner (Agilent Technologies), Scan control software (Agilent Technologies), and Feature extraction software (Agilent Technologies)
|
| Description |
PCC6803 cultured under Light 30 in replicate 2 to check repeatability
|
| Data processing |
The software program Matlab 2013b (The Mathworks Inc., Natick, MA) was used for data analysis. After removing signal intensities that the Feature extraction software judged unreliable, the median of the probe signal intensities representing each ORF was defined as the gene expression level. Quantile normalization [26] was applied to all data sets to allow comparison of the gene expression profiles.
|
| |
|
| Submission date |
Mar 05, 2018 |
| Last update date |
Mar 06, 2018 |
| Contact name |
Kenichi Ogawa |
| E-mail(s) |
[email protected]
|
| Phone |
81-90-6962-9302
|
| Organization name |
Osaka University
|
| Lab |
Metabolic Engineering Lab
|
| Street address |
1-5, Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24690 |
| Series (1) |
| GSE111408 |
Transcriptome analysis of the microalgae Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions |
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