|
| Status |
Public on Aug 15, 2012 |
| Title |
R. sphaeroides pRPcrZ vs. R. sphaeroides pR4352 replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R. sphaeroides PcrZ total cells
|
| Organism |
Cereibacter sphaeroides |
| Characteristics |
sample type: total RNA isolates of R. sphaeroides pRPcrZ
strain: pRPcrZ
growth condition: low oxygen (0.5 mg/L O2)
|
| Growth protocol |
R. sphaeroides strains grown under low oxygen conditions (0,5 mg/L O2).
|
| 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 pR4352 total cells
|
| Organism |
Cereibacter sphaeroides |
| Characteristics |
strain: pR4352
sample type: total RNA isolates of R. sphaeroides pR4352
growth condition: low oxygen (0.5 mg/L O2)
|
| Growth protocol |
R. sphaeroides strains grown under low oxygen conditions (0,5 mg/L O2).
|
| 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 pR4352 and the PcrZ over-expression (pRPcrZ) 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 |
pooled biological sample 1-3
|
| Data processing |
R with Limma package was used for data evaluation. LOWESS normalized and background subtracted.
|
| |
|
| Submission date |
Apr 18, 2012 |
| Last update date |
Sep 11, 2012 |
| 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) |
| GSE37381 |
R. sphaeroides pRKPcrZ vs. R. sphaeroides pRK4352 under low oxygen conditions |
|
