|
| Status |
Public on Oct 22, 2021 |
| Title |
Synechocystis_PCC6803_2h_mock_control_2 |
| Sample type |
RNA |
| |
|
| Source name |
mock 2h 2
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
treatment: mock 2h
|
| Treatment protocol |
Exponentially growing cells (density of 2 x 107 cells ml-1) were transferred to a plastic dish and irradiated with UV-C (254 nm) using UV lamps (UVP Inc., Upland, CA, USA) at a dose rate of 400 J/m2
|
| Growth protocol |
Synechocystis sp. PCC 6803 PCC-M strain (Trautmann, 2012) was grown photoautotrophically (40 µmol photons·m-2·s-1) at 30°C in BG-11 medium (Rippka, 1979) supplemented with 20 mM HEPES-NaOH (pH 7.5).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Synechocystis 6803 cells were harvested by rapid filtration on hydrophilic polyethersulfone filters (Supor 800 Filter, 0.8 μm, Pall, New York, NY, USA). The filter covered with cells was immediately immersed in 1 ml of PGTX solution (Pinto, 2009)and frozen in liquid nitrogen. Total RNA was extracted as described previously (Hein, 2013).
|
| Label |
Cy3
|
| Label protocol |
The DNAse treated 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 G2505C US90900275, 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.
|
| |
|
| Submission date |
Oct 21, 2021 |
| Last update date |
Oct 22, 2021 |
| 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) |
| GSE186330 |
Feedback regulation of RNase E during UV-stress response in cyanobacteria |
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