|
| Status |
Public on Jun 29, 2013 |
| Title |
PCC6803_WT_24h_low_carbon_2 |
| Sample type |
RNA |
| |
|
| Source name |
PCCWT_24h_low_carbon
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
genotype/varitaion: wild type
co2 condition: low (ambient air containing 0.035% CO2)
|
| Treatment protocol |
For CO2-shift experiments, cells were pre-cultivated with air enriched with 5% CO2 (defined as high CO2, HC) in BG11medium of pH 8.0. Then, cells were harvested by centrifugation (5 min at 3000 g, 20°C). The pellet was washed and re-suspended in fresh BG11medium of pH 7.0 at an optical density at 750 nm (OD750) of 0.8. After 1 h cultivation under HC conditions, CO2 limitation was set by shifting the exponentially growing cultures to bubbling with ambient air containing 0.035% CO2 (defined as low CO2, LC).
|
| Growth protocol |
The glucose-tolerant strain Synechocystis sp. PCC 6803 was obtained from N. Murata (National Institute for Basic Biology, Okazaki, Japan) and served as the wild type (WT).Cells were grown photoautotrophically in batch cultures using glass vessels of 3-cm diameter with 5-mm glass tubes for aeration (blubbing flow rate was 5 ml min-1) under continuous illumination of 130 µmol photons m-2s-1 (Osram L58 W 32/3) at 29°C in BG11 medium (Rippka et al., 1979). Cultivation of the mutant Δsml0013::Km was performed in the presence of 50 µgml-1 kanamycin (Km).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from 5 ml of culture were harvested by centrifugation at 4,000 rpm for 5 min at 4°C and were immediately frozen at -80°C. Total RNA was extracted after pre-treatment with hot phenol and chloroform by the High PureRNA isolation kit (Roche Diagnostics).
|
| Label |
Cy3
|
| Label protocol |
The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.
|
| |
|
| Hybridization protocol |
The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA
|
| Scan protocol |
Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocol GE1_107_Sep09 for Cy3 labelled arrays
|
| Description |
WT_24h_LC-2
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
Jun 29, 2013 |
| Contact name |
Jens Georg |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Freiburg
|
| Street address |
Schänzlestr. 1
|
| City |
Freiburg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15867 |
| Series (1) |
| GSE48415 |
The gene sml0013 of Synechocystis sp. strain PCC 6803 encodes for a novel subunit of the NDH1 complex that is ubiquitous distributed among cyanobacteria. |
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