|
| Status |
Public on Nov 14, 2012 |
| Title |
R. sphaeroides WT 2.4.1_7 min singlet oxygen stress versus 0 min stress_transcriptome replicate A |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R. sphaeroides crude extracts_7 min
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
rna fraction: total RNA isolates
time point after stress: 7 min
|
| Growth protocol |
R. sphaeroides WT 2.4.1 was grown under aerobic conditions (100% oxygen) to an OD660 of 0.4 and stressed with 0.2 µM methylene blue in the presence of 800 W m-2 high light
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Transcriptome: Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen). Translatome: Polysome fractions were collected by sucrose density gradient centrifugation and polysomal RNA isolated by the hot phenol method. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
The ULS Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation.
|
| |
|
| Channel 2 |
| Source name |
R. sphaeroides crude extracts_0 min
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
rna fraction: total RNA isolates
time point after stress: 0 min
|
| Growth protocol |
R. sphaeroides WT 2.4.1 was grown under aerobic conditions (100% oxygen) to an OD660 of 0.4 and stressed with 0.2 µM methylene blue in the presence of 800 W m-2 high light
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Transcriptome: Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen). Translatome: Polysome fractions were collected by sucrose density gradient centrifugation and polysomal RNA isolated by the hot phenol method. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
The ULS Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation.
|
| |
|
| |
| Hybridization protocol |
RNA of three independent experiments of Rhodobacter sphaeroides WT 2.4.1 at 7/45/90 min and 0 min 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.
|
| Description |
biological sample 1-3
|
| Data processing |
LOESS normalization (within- and between-arrays) with Limma package for Bioconductor in R was applied for dye-bias correction.
|
| |
|
| Submission date |
Nov 13, 2012 |
| Last update date |
Apr 08, 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 (1) |
| GSE42244 |
Rhodobacter sphaeroides WT 2.4.1 under singlet oxygen stress |
|
