|
| Status |
Public on Aug 01, 2012 |
| Title |
Synechocystis PCC6803, 3h, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Synechocystis PCC6803, 3h after iron limitation stress induction by DFB addition
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
stress: iron limitation
time: 3h
|
| Treatment protocol |
Desferrioxamine B (endconcentration 100µM) was added to the liquid cultures, and samples were taken before treatment, 3,12, 24, 48 and 72 h after DFB addition.
|
| 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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Synechocystis cells (40 to 50 ml) were collected at different time points by rapid filtration (Pall Supor 800 Filter, 0.8 mm). The filters with the collected cells were transferred to a tube containing 2 ml of PGTX (Pinto et al. 2009), immediately frozen in liquid nitrogen and stored at -80°C until extraction. RNA was extracted following the protocol by Pinto et al., 2009 (Pinto, Thapper et al. 2009)
|
| 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 protocols GE1_107_Sep09 and GE1-v1_95_Feb07 for Cy3 labelled arrays
|
| Description |
WT_3h.1
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensity was background corrected (normexp) and quantile normalized.
|
| |
|
| Submission date |
Aug 01, 2012 |
| Last update date |
Aug 01, 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) |
| GSE39804 |
Inference of pathways, non-coding RNAs and regulatory elements during iron deprivation of Synechocystis based on comprehensive expression profiling |
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