|
| Status |
Public on Apr 07, 2011 |
| Title |
Root of MIT Knockdown Plant vs. WT, Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MIT knockdown plant, root
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Dongjing
genotype: MIT knockdown
age: day 35
tissue: root
|
| Growth protocol |
Rice plants were grown in hydroponic solution for 5 weeks under control conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy5
|
| Label protocol |
Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
WT, root
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Dongjing
genotype: WT
age: day 35
tissue: root
|
| Growth protocol |
Rice plants were grown in hydroponic solution for 5 weeks under control conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides.
|
| Description |
Replicate 2 of 2. Root of WT vs. root of MIT knockdown plant.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.
|
| |
|
| Submission date |
Apr 06, 2011 |
| Last update date |
Apr 07, 2011 |
| Contact name |
Yasuhiro Ishimaru |
| E-mail(s) |
yasrnr@m.tohoku.ac.jp
|
| Phone |
+81-22-795-6557
|
| Fax |
+81-22-795-6557
|
| Organization name |
Tohoku University
|
| Street address |
6-3 Aramakiaza-aoba, Aoba-ku, Sendai
|
| City |
Miyagi |
| ZIP/Postal code |
980-8578 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE28428 |
Rice plants (Oryza sativa var. japonica): WT vs. MIT knockdown plant |
|
