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| Status |
Public on Oct 10, 2012 |
| Title |
PCC6803_Wt+empty_plasmid_0h_copper depletion_2 |
| Sample type |
RNA |
| |
|
| Source name |
PCC6803_Wt+empty_plasmid_0h_copper depletion_2
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
genotype: WT
|
| Treatment protocol |
For induction of the PpetJ promoter CuSO4 was omitted from the medium, cells were first washed for two times, and then resuspended in copper-free medium. Cultures were incubated in copper-free medium for the indicated time. Repression was achieved by adding 2.5-5 µM CuSO4 to the medium.
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| Growth protocol |
The Synechocystis 6803 WT strain used in this study was provided by S. Shestakov (Moscow State University, Russia) and was propagated on BG11 (Rippka et al., 1979) containing 0.75% (w/v) agar (Bacto agar, Difco) plates. Liquid cultures of WT and mutant strains were grown in BG11 medium containing 10 mM TES buffer (pH 8.0) under continuous illumination with white light of 40 µmol photons•m–2•s–1 at 30°C or at 120 µmol photons•m–2•s–1 for high light treatment. Media for mutant strains were supplemented with 40 µg mL–1 kanamycin (Km), 20 µg mL–1 spectinomycin (Spec), or a combination of 40 µg mL–1 kanamycin and 20 µg mL–1 spectinomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Synechocystis 6803 liquid cultures were collected by quenching on ice and immediate centrifugation at 4 °C. RNA was extracted following the protocol by Pinto et al., 2009 (Pinto, Thapper et al. 2009) with an additional phenol/chloroform/Isoamyl alcohol (25:24:1 v/v) extraction preceding the RNA precipitation.
|
| 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.
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| |
|
| 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 protocols GE1_107_Sep09 for Cy3 labelled arrays.
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.
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| |
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| Submission date |
Oct 09, 2012 |
| Last update date |
Oct 10, 2012 |
| 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) |
| GSE41411 |
The small RNA PsrR1 affects oligomerization of photosystem I by post-transcriptional repression of psaL in Synechocystis sp. PCC6803 |
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