|
| Status |
Public on May 23, 2013 |
| Title |
R. sphaeroides 2.4.1 -Fe vs. R. sphaeroides 2.4.1 replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R. sphaeroides 2.4.1 -Fe total cells
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
culture: anaerobic without iron
|
| Treatment protocol |
R. sphaeroides was grown anaerobically without external iron but with the iron chelator 2,2’-dipyridyl (30 µM). Anaerobic growth was provided using dimethyl sulfoxide (DMSO) as electron acceptor at a final concentration of 60 mM.
|
| Growth protocol |
R. sphaeroides strains grown anaerobically in presence and absence of iron
|
| 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 |
culture: anaerobic with iron
|
| Treatment protocol |
R. sphaeroides was grown anaerobically without external iron but with the iron chelator 2,2’-dipyridyl (30 µM). Anaerobic growth was provided using dimethyl sulfoxide (DMSO) as electron acceptor at a final concentration of 60 mM.
|
| Growth protocol |
R. sphaeroides strains grown anaerobically in presence and absence of iron
|
| 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 2.4.1 under iron limitation and normal (control) conditions 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 |
biological sample 4-6
|
| Data processing |
R with Limma package was used for data evaluation. LOWESS normalized and background subtracted.
|
| |
|
| Submission date |
May 22, 2013 |
| Last update date |
May 23, 2013 |
| 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 (2) |
| GSE47182 |
Comparative analysis of the response to iron-limitation in the absence of oxygen in R. sphaeroides [Microarray] |
| GSE47450 |
Comparative analysis of the response to iron-limitation in the absence of oxygen in R. sphaeroides |
|
