|
Status |
Public on Nov 14, 2012 |
Title |
R. sphaeroides WT 2.4.1_45 min singlet oxygen stress versus 0 min stress_transcriptome replicate B |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
R. sphaeroides crude extracts_45 min
|
Organism |
Cereibacter sphaeroides 2.4.1 |
Characteristics |
rna fraction: total RNA isolates time point after stress: 45 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 4-6
|
Data processing |
LOESS normalization (within- and between-arrays) with Limma package for Bioconductor in R was applied for dye-bias correction.
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|
|
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 |
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