|
| Status |
Public on Nov 09, 2011 |
| Title |
Δirr -Fe vs. Δirr +Fe - microaerobic conditions - replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Δirr - Fe (total cells)
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
growth condition: -Fe (iron limited)
|
| Growth protocol |
R. sphaeroides strains grown microaerobically (30 µM oxygen) to an OD660 = 0.4 either under normal iron conditions or under iron limitation conditions.
|
| 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.
|
| |
|
| Channel 2 |
| Source name |
Δirr + Fe (total cells)
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
growth condition: +Fe (normal)
|
| Growth protocol |
R. sphaeroides strains grown microaerobically (30 µM oxygen) to an OD660 = 0.4 either under normal iron conditions or under iron limitation conditions.
|
| 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.
|
| |
|
| |
| Hybridization protocol |
The RNA of three independent experiments of the Rhodobacter sphaeroides irr deletion mutant (Δ3179) under normal iron (+Fe) and iron limitation (-Fe) 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 pooled
|
| Data processing |
R with Limma package was used for data evaluation. LOWESS normalized and background subtracted.
|
| |
|
| Submission date |
Nov 08, 2011 |
| 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 |
GPL14796 |
| Series (2) |
| GSE33533 |
R. sphaeroides Δirr -Fe vs. R. sphaeroides Δirr +Fe under microaerobic conditions |
| GSE33535 |
Transcriptional profiling of R. sphaeroides Δirr |
|
