|
| Status |
Public on Jan 30, 2014 |
| Title |
CS_standard_biol.rep4 (reanalysis) |
| Sample type |
RNA |
| |
|
| Source name |
cells from control strain, standard growth conditions, biological replicate 4
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
strain: control strain
phenotype: glucose tolerant
treatment protocol: standard growth conditions
|
| Growth protocol |
Cell were grown in BG-11 medium in standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959). RNA was purified and DNase treated using RNeasy mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.
|
| Scan protocol |
Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).
|
| Description |
GSM1213401
|
| Data processing |
The scanned images were analyzed with Agilent's Feature Extraction program version 10.7.3. using protocol GE1_107_Sep09 and Grid 016989_D_F_20070606. gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method.
|
| |
|
| Submission date |
Oct 24, 2013 |
| Last update date |
Jul 16, 2014 |
| Contact name |
Taina Tyystjarvi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Turku
|
| Department |
Biochemistry
|
| Lab |
Molecular Plant Biology
|
| Street address |
Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor
|
| City |
Turku |
| ZIP/Postal code |
20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL17595 |
| Series (2) |
| GSE51647 |
The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria |
| GSE59451 |
The ω subunit of RNA polymerase is essential for thermal acclimation of the Cyanobacterium Synechocystis sp. PCC 6803 |
|
| Relations |
| Reanalysis of |
GSM1213401 |
