|
| Status |
Public on Mar 23, 2020 |
| Title |
Δcph2-48h_blue-light-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
cells from liquid culture grown 48h under 5 µmols photons m-2 s-1 of blue light
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
strain: delta-cph2 lacking bacteriophytochrome Cph2
|
| Treatment protocol |
Cultures were diluted to the same optical density at 750nm with BG11 medium supplemented with 11 mM glucose and 10 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES)-KOH at pH 8.0 and grown further for 48h under 5 µmols photons m-2 s-1 of blue light (Lee filter #119, dark blue) or green light (Lee filter #089, moss green).
|
| Growth protocol |
Wild-type and Δcph2 strains were grown in BG11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) in Erlenmeyer flasks and supplemented with 10 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES)-KOH at pH 8.0 at 50 µmols photons m-2 s-1 of white light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in 1.6 ml PGTX, with the following composition: 39.6% (w/v) phenol, 7% (v/v) glycerol, 7 mM 8-hydroxyquinoline, 20 mM EDTA, 97.5 mM sodium acetate, 0.8 M guanidine-thiocyanate, and 0.48 M guanidine hydrochloride (Pinto et al., 2009; BMC Mol Biol 10: 79). Phenol was extracted twice with 1-Bromo-3-chloropropane and RNA was precipitated with isopropanol at -20°C, followed by centrifugation at 4°C. The RNA pellet was washed with 70% ethanol and resuspended in RNase-free A. dest.
|
| Label |
Cy3
|
| Label protocol |
Aliquots of three micrograms of DNA-depleted total-RNA was labeled directly 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 protocol GE1_107_Sep09 for Cy3 labelled arrays
|
| Description |
gene expression after light treatment for 48h
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.
|
| |
|
| Submission date |
Jun 28, 2018 |
| Last update date |
Mar 24, 2020 |
| Contact name |
Thomas Wallner |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Freiburg
|
| Department |
Institute of Biology III
|
| Lab |
AG Wilde - Molecular Genetics of Prokaryotes
|
| Street address |
Schaenzlestrasse 1
|
| City |
Freiburg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15867 |
| Series (1) |
| GSE116409 |
The cyanobacterial phytochrome 2 regulates the expression of motility-related genes through the second messenger cyclic di-GMP |
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