|
| Status |
Public on Jan 11, 2011 |
| Title |
WT plants-1h vs 0h HL-Rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT, 0h HL
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: WT
treatment: none
time: 0 hour
plant age: 21 days
|
| Treatment protocol |
3- to 4-week-old plants (at the same developmental stage of 1.09-1.10, Boyes et al., 2001) were exposed to a continuous high light irradiation (1000 μmol.m-2.s-1) in a SANYO growth cabinet for 0 or 1 hour.
|
| Growth protocol |
Arabidopsis thaliana plants were grown on Jiffy-7 soil pellets (Jiffy Products, Norway) in a controlled growth chamber (Weiss technik) at 21-22 °C, 16 h/8 h light regime at 100 μmol.m-2 s-1 photoperiod and 70% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From two independent experiments, RNA was isolated from middle-aged leaves of 25 wild type (WT), apx1, cat2, and apx1/cat2 plants using TRIzol Reagent (Invitrogen, Carlsbad, CA). Concentration and quality of the RNA was determined with a Nanodrop ND 1000 spectrophotometer and quality was examined using the RNA 6000 Nano Assay (Agilent Technologies 2100 Bioanalyzer).
|
| Label |
Cy5
|
| Label protocol |
Per sample, an amount of 1 µg of total RNA was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| Channel 2 |
| Source name |
WT, 1h HL
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: WT
treatment: high light irradiation
time: 1 hour
plant age: 21 days
|
| Treatment protocol |
3- to 4-week-old plants (at the same developmental stage of 1.09-1.10, Boyes et al., 2001) were exposed to a continuous high light irradiation (1000 μmol.m-2.s-1) in a SANYO growth cabinet for 0 or 1 hour.
|
| Growth protocol |
Arabidopsis thaliana plants were grown on Jiffy-7 soil pellets (Jiffy Products, Norway) in a controlled growth chamber (Weiss technik) at 21-22 °C, 16 h/8 h light regime at 100 μmol.m-2 s-1 photoperiod and 70% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From two independent experiments, RNA was isolated from middle-aged leaves of 25 wild type (WT), apx1, cat2, and apx1/cat2 plants using TRIzol Reagent (Invitrogen, Carlsbad, CA). Concentration and quality of the RNA was determined with a Nanodrop ND 1000 spectrophotometer and quality was examined using the RNA 6000 Nano Assay (Agilent Technologies 2100 Bioanalyzer).
|
| Label |
Cy3
|
| Label protocol |
Per sample, an amount of 1 µg of total RNA was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| |
| Hybridization protocol |
A mixture of purified and labeled cRNA was hybridised on Agilent arrays followed by (manual) washing, according to the manufacturer’s procedures.
|
| Scan protocol |
Arrays were scanned using the Agilent DNA MicroArray Scanner.
Images were quantified using Agilent Feature Extraction Software (version 8.1.1.1).
|
| Description |
Biological replicate 2 of 2. WT plants subjected to high light, harvested after 0h and 1h.
|
| Data processing |
Features were extracted with spatial detrending and dye normalization (Linear Lowess) using the Agilent Feature Extraction Software (version 8.1.1.1).
|
| |
|
| Submission date |
Jan 12, 2010 |
| Last update date |
Jan 11, 2011 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL2871 |
| Series (1) |
| GSE19857 |
Functional characterization of Arabidopsis mutants deficient in cytosolic APX1 and peroxisomal CAT2 |
|
