|
| Status |
Public on Apr 30, 2008 |
| Title |
Cu_treatment_10µM_3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Oryza sativa leaf treated with 10 µM Cu for 1 day
|
| Organism |
Oryza sativa |
| Characteristics |
Oryza sativa L. cv. Nipponbare leaf treated with 10 µM Cu for 1 day
|
| Treatment protocol |
Rice plants (Oryza sativa L. cv. Nipponbare) were grown hydroponically (Kamachi et al. (1991) Plant Physiol. 96, 411-417.) in an environment-controlled greenhouse with a photoperiod of 12 h light (25 to 28˚C) for 6 to 7 weeks. Three rice plants were grown in each 500-ml plastic pot containing a nutrient solution which was renewed once a week. Rice plants whose 8th leaf was fully expanded were used for experimental treatments. Rice plants which had been grown as described above were treated with hydroponic solutions containing 10 µM CuCl2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from three different leaf samples per treatment using an RNeasy® Plant Mini Kit (Qiagen, Hilden, Germany).
|
| Label |
Cy5
|
| Label protocol |
Cy3- and Cy5-labeled cRNA was prepared from 400 ng of total RNA from rice leaves, using a Low RNA Input Linear Amplification Kit (Agilent Technologies, Inc., Palo Alto, CA, USA) and Cy3- and Cy5-CTP (Perkin Elmer). Labeled cRNA was purified with RNeasy mini spin columns (Qiagen).
|
| |
|
| Channel 2 |
| Source name |
Oryza sativa leaf treated with 0.3 µM Cu (control) for 1 day
|
| Organism |
Oryza sativa |
| Characteristics |
Oryza sativa L. cv. Nipponbare leaf treated with 0.3 µM Cu (control) for 1 day
|
| Treatment protocol |
Rice plants (Oryza sativa L. cv. Nipponbare) were grown hydroponically (Kamachi et al. (1991) Plant Physiol. 96, 411-417.) in an environment-controlled greenhouse with a photoperiod of 12 h light (25 to 28˚C) for 6 to 7 weeks. Three rice plants were grown in each 500-ml plastic pot containing a nutrient solution which was renewed once a week. Rice plants whose 8th leaf was fully expanded were used for experimental treatments. Rice plants which had been grown as described above were treated with normal hydroponic solutions containing 0.3 µM CuCl2 as the control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from three different leaf samples per treatment using an RNeasy® Plant Mini Kit (Qiagen, Hilden, Germany).
|
| Label |
Cy3
|
| Label protocol |
Cy3- and Cy5-labeled cRNA was prepared from 400 ng of total RNA from rice leaves, using a Low RNA Input Linear Amplification Kit (Agilent Technologies, Inc., Palo Alto, CA, USA) and Cy3- and Cy5-CTP (Perkin Elmer). Labeled cRNA was purified with RNeasy mini spin columns (Qiagen).
|
| |
|
| |
| Hybridization protocol |
One microgram of Cy3-labeled cRNA was mixed with the same amount of Cy5-labeled cRNA and used for subsequent hybridization. Hybridization was carried out for 17 h with rotation at 60˚C.
|
| Scan protocol |
Slides were scanned using a GenePix 4000A scanner (Axon Instruments Inc., Foster City, CA, USA) with 550 V and 680 V of PMT voltage for Cy3 and Cy5 detection, respectively.
|
| Description |
Oryza sativa leaf treated with 10 µM Cu for 1 day, replicate 3
|
| Data processing |
DATA were quantified by Microarray Suite 2.0 (IPLab Spectrum Software, Scanalytics, Fairfax, VA, USA)
|
| |
|
| Submission date |
Apr 02, 2008 |
| Last update date |
Oct 28, 2008 |
| Contact name |
Hitoshi Sakakibara |
| E-mail(s) |
sakaki@riken.jp
|
| Phone |
81-45-503-9576
|
| Fax |
81-45-503-9609
|
| Organization name |
RIKEN
|
| Department |
Plant Science Center
|
| Lab |
Biodynamics Research Team
|
| Street address |
1-7-22 Suehiro, Tsurumi
|
| City |
Yokohama |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL892 |
| Series (1) |
| GSE11021 |
Gene Expression in Response to excess Copper Stress in Rice Leaves |
|
