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| Status |
Public on Oct 01, 2016 |
| Title |
PCC6803_[delta]isaR1_3h_DFB_addition_2 |
| Sample type |
RNA |
| |
|
| Source name |
Synechocystis 6803 liquid cultures
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
timepoint: 3h
treatment: Desferrioxamine B (endconcentration 100µM)
genotype: [delta]isaR1
|
| Treatment protocol |
Desferrioxamine B (endconcentration 100µM) was added to the liquid cultures, and samples were taken before treatment and 3,12, 24, 48 and 72 h after DFB addition. IsaR1 overexpression was induced by addition of CuSO4 to a final concentration of 2 µM.
|
| Growth protocol |
Synechocystis wild type strain was grown at 30 °C in a modified version of BG11 medium (YBG11) containing a higher amount of EDTA (16 μM instead of 2.8 μM in BG11) and a lower iron concentration (Shcolnick, Shaked et al. 2007). Light intensity was adjusted to 50 μmol photons m−2·s−1 of white light. Cultures were aerated with normal air for the iron stress experiment and shaked without aeration for the overexpression experiment. IsaR1OE and WT_pVZ were grown in presence of 2 µg mL-1 gentamicin.
|
| 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 for the iron depletion Experiment. For the overexpression experiment a G2505C scanner was used with the same Software and protocol version.
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensity was normexp background substracted and quantile normalized.
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| |
|
| Submission date |
Sep 29, 2016 |
| Last update date |
Oct 01, 2016 |
| 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) |
| GSE87496 |
Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteria |
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