|
| Status |
Public on Nov 26, 2015 |
| Title |
R. sphaeroides 2.4.1 (trans) vs. R. sphaeroides 2.4.1 (exp aerob) 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
transition phase_aerobic
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
growth phase: transition phase
aeration condition: aerobic
|
| Treatment protocol |
R. sphaeroides strains grown under low aeration or aerobic conditions and cells were harvested at different growth phases
|
| Growth protocol |
R. sphaeroides strains grown under low aeration or aerobic 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
|
| |
|
| Channel 2 |
| Source name |
exponential phase_aerobic
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
growth phase: exponential phase
aeration condition: aerobic
|
| Treatment protocol |
R. sphaeroides strains grown under low aeration or aerobic conditions and cells were harvested at different growth phases
|
| Growth protocol |
R. sphaeroides strains grown under low aeration or aerobic 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
|
| |
|
| |
| Hybridization protocol |
Total RNA of three independent experiments (biological replicates 1-3 or 4-6) of two different growth phases were pooled and hybridized to one array. Two arrays were hybridized with independent experimental runs. 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 |
1 trans vs exp (aerob)
biological sample 1-3
|
| Data processing |
LOESS normalization log2 ratio (Cy3/Cy5) with Limma package (v.3.14.3; release date: 2012/11/29) for Bioconductor in R
|
| |
|
| Submission date |
Nov 24, 2015 |
| Last update date |
Nov 26, 2015 |
| 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) |
| GSE75345 |
Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides |
|
