|
| Status |
Public on Apr 07, 2011 |
| Title |
wild type vs mutant_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Coleoptile of wild type seeds germinated under submergence
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype/variation: wild type
cultivars: Kinmaze
|
| Treatment protocol |
Seedling were fixed with ethanol : acetic acid (3:1). Then, seedlings, which were embedded in RNase-free water, were frozen in hexane cooled with dry ice and stored at -80℃. We cut frozen section of 8 µm thickness. Coleoptiles were isolated from sections by laser microdissection.
|
| Growth protocol |
15 seeds were sowed in 1 L glass bottle filed with 1 L deionized water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell type and tissue with a PicoPure™ RNA isolation kit (Molecular Devices, Ontario, Canada) following the manufacturer's recommendations. The qualities of the RNA samples were assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cy3and Cy5-labeled cRNA were prepared from total RNA using Low RNA Input Linear Amplification Kit (Agilent) in accordance with the manufacturer's protocol with slight modification.
|
| |
|
| Channel 2 |
| Source name |
Coleoptile of mutant seeds germinated under submergence
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype/variation: rad mutant
cultivars: Kinmaze
|
| Treatment protocol |
Seedling were fixed with ethanol : acetic acid (3:1). Then, seedlings, which were embedded in RNase-free water, were frozen in hexane cooled with dry ice and stored at -80℃. We cut frozen section of 8 µm thickness. Coleoptiles were isolated from sections by laser microdissection.
|
| Growth protocol |
15 seeds were sowed in 1 L glass bottle filed with 1 L deionized water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell type and tissue with a PicoPure™ RNA isolation kit (Molecular Devices, Ontario, Canada) following the manufacturer's recommendations. The qualities of the RNA samples were assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy5
|
| Label protocol |
Cy3and Cy5-labeled cRNA were prepared from total RNA using Low RNA Input Linear Amplification Kit (Agilent) in accordance with the manufacturer's protocol with slight modification.
|
| |
|
| |
| Hybridization protocol |
Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). cRNA was hybridized to microarray using hybridization oven G2531A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.
|
| Scan protocol |
Microarrays were scanned using Agilent DNA microarray scanner G2505B according to manufacturer's instructions.
|
| Description |
Gene expression in the rice coleoptile between wild type and mutant
|
| Data processing |
Scanned tiff image files were analyzed with FeatureExtraction 8.5.1.1 (Agilent). We used the linear & lowess methods for normalization.
|
| |
|
| Submission date |
Jan 14, 2011 |
| Last update date |
Apr 07, 2011 |
| Contact name |
Hirokazu Takahashi |
| E-mail(s) |
aa087005@mail.ecc.u-tokyo.ac.jp
|
| Phone |
+81-3-5841-5075
|
| Organization name |
University of Tokyo
|
| Department |
Graduate school of agricultural and life Science
|
| Lab |
Laboratory of Plant Molecular Genetics
|
| Street address |
1-1-1 Yayoi, Bunkyo
|
| City |
Tokyo |
| ZIP/Postal code |
113-8657 |
| Country |
Japan |
| |
|
| Platform ID |
GPL892 |
| Series (1) |
| GSE26632 |
Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant |
|
