|
| Status |
Public on Oct 26, 2011 |
| Title |
R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 - blue light conditions - replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R. sphaeroides Δlov total cells
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
genotype/variation: Δlov
growth protocol: blue light, semiaerobic conditions
|
| Growth protocol |
R. sphaeroides strains grown semiaerobically (90 µM O2) under blue light illumination (20 µmol m-2 s-1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation
|
| |
|
| Channel 2 |
| Source name |
R. sphaeroides 2.4.1 total cells
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
genotype/variation: wild type
growth protocol: blue light, semiaerobic conditions
|
| Growth protocol |
R. sphaeroides strains grown semiaerobically (90 µM O2) under blue light illumination (20 µmol m-2 s-1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation
|
| |
|
| |
| Hybridization protocol |
The RNA of three independent experiments of Rhodobacter sphaeroides wild type and the Δlov deletion mutant were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.
|
| Scan protocol |
Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)
|
| Description |
Lov1 blue light
biological sample 1-3
|
| Data processing |
R with Limma package was used for data evaluation. LOWESS normalized and background subtracted.
|
| |
|
| Submission date |
Oct 26, 2011 |
| Last update date |
Oct 26, 2011 |
| Contact name |
Sebastian Harald Michael Metz |
| E-mail(s) |
Sebastian.Metz@mikro.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-Universität Giessen
|
| Department |
Institut für Mikro- und Molekularbiologie
|
| Lab |
Klug
|
| Street address |
Heinrich-Buff-Ring 26-32
|
| City |
Giessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL14796 |
| Series (2) |
| GSE33259 |
R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (blue light, semiaerobic conditions) |
| GSE33261 |
Role of a short LOV protein in blue light- and singlet oxygen-dependent gene regulation in Rhodobacter sphaeroides |
|
