|
| Status |
Public on Nov 18, 2014 |
| Title |
R. sphaeroides 2.4.1 (pBBRSorYi) vs. R. sphaeroides 2.4.1 (pBBR) replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R. sphaeroides 2.4.1, 10min 1O2, total cells
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
test: total RNA isolates of R. sphaeroides 2.4.1 (pBBRSorYi), 10min 1O2
|
| Treatment protocol |
R. sphaeroides was grown aerobically. Photooxidative stress conditions were generated by the addition of methylene blue (0.2 µM) and exposure to white light (800wm-2) for 10min
|
| Growth protocol |
R. sphaeroides strains grown aerobically
|
| 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, 10min 1O2, total cells
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
reference: total RNA isolates of R. sphaeroides 2.4.1 (pBBR), 10min 1O2
|
| Treatment protocol |
R. sphaeroides was grown aerobically. Photooxidative stress conditions were generated by the addition of methylene blue (0.2 µM) and exposure to white light (800wm-2) for 10min
|
| Growth protocol |
R. sphaeroides strains grown aerobically
|
| 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 |
Total RNA of three independent experiments of a SorY overexpressing strain (2.4.1pBBRSorYi) and a control strain harbouring an empty vector (2.4.1pBBR) after 10 min of 1O2 stress, were pooled and hybridized to one array. Two arrays werehybridized with independent experimental runs. 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 |
biological sample 4-6
|
| Data processing |
R with Limma package was used for data evaluation. LOESS normalized and background subtracted.
|
| |
|
| Submission date |
Nov 17, 2014 |
| Last update date |
Nov 18, 2014 |
| Contact name |
Gabriele Klug |
| E-mail(s) |
[email protected]
|
| Organization name |
Justus-Liebig University Gießen
|
| Department |
Molecular- and Microbiology
|
| Street address |
Heinrich-Buff-Ring 26-32
|
| City |
Gießen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15457 |
| Series (1) |
| GSE63328 |
The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides |
|
