|
| Status |
Public on Jan 01, 2017 |
| Title |
R. sphaeroides WT 2.4.1_pRKSorX144 versus pRK415 after 7 min of singlet oxygen stress_biological replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R. sphaeroides crude extracts_pRKSorX144 7 min
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
genotype/variation: pRKSorX144
|
| Growth protocol |
R. sphaeroides strains were grown under aerobic conditions (100% oxygen) to an OD660 of 0.4 and stressed with 0.2 µM methylene blue in the presence of 800 W m-2 high light for 7 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen).
|
| 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 crude extracts_pRK415 7 min
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
genotype/variation: pRK415
|
| Growth protocol |
R. sphaeroides strains were grown under aerobic conditions (100% oxygen) to an OD660 of 0.4 and stressed with 0.2 µM methylene blue in the presence of 800 W m-2 high light for 7 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen).
|
| 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 Rhodobacter sphaeroides 2.4.1 pRKSorX144 and pRK415 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.
|
| Description |
biological sample 4-6
|
| Data processing |
LOESS normalization with Limma package for Bioconductor in R was applied for dye-bias correction.
|
| |
|
| Submission date |
Mar 21, 2016 |
| Last update date |
Jan 01, 2017 |
| Contact name |
Gabriele Klug |
| E-mail(s) |
Gabriele.Klug@mikro.bio.uni-giessen.de
|
| 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) |
| GSE79421 |
Rhodobacter sphaeroides 2.4.1 pRKSorX144 versus pRK415 under singlet oxygen stress. |
|
