|
| Status |
Public on Jan 27, 2011 |
| Title |
axe1-5, Untreated plants, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Untreated Arabidopsis axe1-5 plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype/variation: hda6 mutant axe1-5
tissue: Whole plants
age: 14 day old seedlings
|
| Treatment protocol |
The plants were treated with or without 3 days of cold treatment ( at 2°C, 12 h light / 12 h dark).
|
| Growth protocol |
Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing MS agar (0.85%) medium supplemented with 1% sucrose for 14 days under 16-h-light/8-h-dark (40-80 μmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from the plants before or after cold treatment (at 2°C for 3days) using Plant RNA Purification Reagent (Invitrogen) according to manufacture’s instruction.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.
|
| Description |
Gene expression data from untreated axe1-5 plants
|
| Data processing |
The scanned images were analyzed with GeneSpring ver.7 (Agilent). Percentile normalization (75 percentile) was performed for each chip.
|
| |
|
| Submission date |
Jan 26, 2011 |
| Last update date |
Jul 29, 2016 |
| Contact name |
Motoaki Seki |
| E-mail(s) |
motoaki.seki@riken.jp
|
| Organization name |
RIKEN CSRS
|
| Street address |
1-7-22, Suehiro-cho, Tsurumi
|
| City |
Yokohama |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9020 |
| Series (1) |
| GSE26873 |
Expression data in Arabidopsis hda6 mutant axe1-5 and its parental line DR5 under cold and control conditions. |
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