|
| Status |
Public on May 20, 2009 |
| Title |
Dark_4 |
| Sample type |
RNA |
| |
|
| Source name |
Synechocystis PCC6803 culture raised under dark conditions
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
stress: Dark
|
| Treatment protocol |
Different stress conditions were applied to exponentially growing cultures of Synechocystis 6803 as follows: For high light stress, light intensity was shifted from 50 to 500 μmol of photons•m–2•s–1 for 30min. Another culture was harvested after 1 h incubation in the dark. For CO2-depletion culture was centrifuged and washed one time with BG11 (20mM TES pH 7.0) w/o NaCO2. Culture was harvested after 6h in the CO2 depletion medium without a stream of air.
|
| Growth protocol |
Standard growth conditions: Liquid cultures of Synechocystis 6803 were grown at 30°C in BG11 (20mM TES pH 7.6) medium under continuous illumination with white light of 50 μmol of photons•m–2•s–1 and a continuous stream of air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Synechocystis 6803 cells were collected by rapid filtration (Pall Supor 800 Filter, 0,8 µm). Filters with cells were dissolved in 1 ml TRIzol (Invitrogen) per 40 ml culture, immediately frozen in liquid nitrogen and incubated 15 min at 65 °C in a water bath. Further RNA isolation followed the manufacturer’s protocol.
|
| 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 1.5 µg of labeled RNA.
|
| Scan protocol |
Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.5.1.1 and the protocol GE1-v5_105_DEC08 for Cy3 labelled arrays.
|
| Description |
no additional information
|
| Data processing |
The medians of the raw data were quantile-normalized using the Bioconductor package “limma” .
|
| |
|
| Submission date |
May 19, 2009 |
| Last update date |
May 20, 2009 |
| Contact name |
Bjoern Voss |
| Organization name |
University of Freiburg
|
| Department |
Institute of Biology III
|
| Lab |
Genetics
|
| Street address |
Schänzlestr. 1
|
| City |
Freiburg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL8567 |
| Series (1) |
| GSE16162 |
Differential expression of whole transcriptome in Synechocystis sp. PCC 6803 |
|
