|
| Status |
Public on Nov 09, 2011 |
| Title |
R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R. sphaeroides Δirr (total cells)
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
genotype/variation: irr deletion mutant (Δirr)
|
| Growth protocol |
Cells grown to an OD660=0.4 under microaerobic (30 µM oxygen) 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 fragmentatio.n
|
| |
|
| Channel 2 |
| Source name |
R. sphaeroides 2.4.1 (total cells)
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
genotype/variation: wild type
|
| Growth protocol |
Cells grown to an OD660=0.4 under microaerobic (30 µM oxygen) 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 fragmentatio.n
|
| |
|
| |
| Hybridization protocol |
The RNA of three independent experiments of Rhodobacter sphaeroides wild type and the irr deletion mutant (Δ3179) 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 1-3 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) |
[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 |
GPL14796 |
| Series (2) |
| GSE33534 |
R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 under microaerobic conditions |
| GSE33535 |
Transcriptional profiling of R. sphaeroides Δirr |
|
