|
| Status |
Public on Feb 15, 2013 |
| Title |
ahp2,3,5, droughted, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
ahp2,3,5, droughted, replicate 1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype: ahp2,3,5
tissue: rosette leaves
age: 31 day-old
treatment: droughted
|
| Treatment protocol |
The three week-old plants were exposed to drought stress for 10 days or grown under well-watered condition in parallel.
|
| Growth protocol |
Two-week-old WT and ahk2,3,5 mutant plants (Columbia ecotype) were transferred from GM plates to soil and grown for an additional week (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’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.
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| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer's 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 droughted ahp2,3,5
|
| Data processing |
The scanned images were analyzed with GeneSpring GX11.5.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.
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| |
|
| Submission date |
Nov 14, 2012 |
| Last update date |
Feb 15, 2013 |
| Contact name |
Rie Nishiyama |
| Organization name |
RIKEN
|
| Department |
Plant Science Center
|
| Lab |
Signaling Pathway Research Unit
|
| Street address |
Suehiro-cho 1-7-22, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE42290 |
Expression data in an Arabidopsis cytokinin (CK)-signaling mutant, ahp2,3,5 and its wild type plant (Col-0) under drought and well-water (control) conditions. |
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