|
| Status |
Public on Jun 29, 2013 |
| Title |
PCC6803_WT_standard_conditions_rep_1 |
| Sample type |
RNA |
| |
|
| Source name |
WT_standard_conditions
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
media type: Control media; 10 μM Fe and 1 μM Mn
|
| Treatment protocol |
Prior to an experiment, cultures were spun down and washed in a 20 mM of 2-(N-morpholino) ethanesulfonic acid (MES) and 10 mM ethylenediaminetetraacetic acid (EDTA; Kd, 10^24) pH 5.0 buffer, in order to remove excess metal ions. Cultures where resuspended in one of four media types: 1) Control media; 10 μM Fe and 1 μM Mn. 2) 0Mn; Mn was omitted from the media. 3) 0Fe; Fe was omitted form the media and 50 μM of the siderophore deferoxamine B (DFB; Kd, 1030) were added (Kranzler et al., 2011). 4) 0Fe0Mn; contained DFB and no added Mn or Fe.
|
| Growth protocol |
Synechocystis 6803 was grown in modified BG11 medium (YBG11; Shcolnick et al.,2007) in glass Erlenmeyer flasks. Cultures were maintained under constant shaking,illuminated with 60 μmol photons m-2 s-1 at 30C. Prior to an experiment, cultures were spun down and washed in a 20 mM of 2-(N-morpholino) ethanesulfonic acid (MES) and 10 mM ethylenediaminetetraacetic acid (EDTA; Kd, 1024) pH 5.0 buffer, in order to remove excess metal ions. Cultures where resuspended in one of four media types: 1) Control media; 10 μM Fe and 1 μM Mn. 2) 0Mn; Mn was omitted from the media. 3) 0Fe; Fe was omitted form the media and 50 μM of the siderophore deferoxamine B (DFB; Kd, 1030) were added (Kranzler et al., 2011). 4) 0Fe0Mn; contained DFB and no added Mn or Fe.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures used for microarray analysis were centrifuged at 9,000 g at 4 0C, resuspended in phenol-chloroform extraction and frozen.
|
| 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 protocol GE1_107_Sep09 for Cy3 labelled arrays
|
| Description |
control_1
|
| Data processing |
Raw expression data were subjected to a background correction by subtraction using the R package limma. The raw arrays were normalized using cyclic loess normalization using the normalizeBetweenArrays function of limma. Due to strong deviations in one of the three repeats for the 0Mn and 0Fe0Mn conditions, the corresponding replicates were excluded from further analysis.
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| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
Jun 29, 2013 |
| 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) |
| GSE48416 |
The hierarchy of transition metal homeostasis: Iron controls manganese accumulation in a unicellular cyanobacterium. |
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