|
| Status |
Public on Dec 19, 2016 |
| Title |
PCC6803_WT_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
cells from liquid culture grown at standard conditions
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
genotype/variation: WT
|
| Treatment protocol |
Synechocystis 6803 cells were collected by rapid filtration on hydrophilic polyethersulfone filters (Pall Supor 800 Filter, 0.8 µm).
|
| Growth protocol |
A glucose tolerant strain of Synechocystis sp. PCC 6803 (a kind gift from Prof. Donald A. Bryant) was used as WT and to generate the ΔpmgA strain. WT and ΔpmgA were cultivated in BG-11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) buffered with 20 mM HEPES-NaOH to pH 8.0. The cultures were continuously bubbled with air supplemented with 3% (v/v) CO2 and grown at 30°C at a standard light intensity of 50 μmol photons m–2 s–1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA) and treated with TURBO DNase (Invitrogen, CA, USA).
|
| 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 for Cy3 labelled arrays.
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.
|
| |
|
| Submission date |
Jan 22, 2016 |
| Last update date |
Dec 19, 2016 |
| Contact name |
Stephan Klähn |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Freiburg
|
| Department |
Institute of Biology III
|
| Lab |
Genetics & Experimental Bioinformatics
|
| Street address |
Schänzlestrasse 1
|
| City |
Freiburg |
| State/province |
Baden-Würtemberg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15867 |
| Series (1) |
| GSE77118 |
Photomixotrophic growth protein A (PmgA) regulates carbohydrate metabolism through the non-coding RNA Ncr0700/PmgR1 in the cyanobacterium Synechocystis sp. PCC 6803 |
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