|
| Status |
Public on Oct 02, 2012 |
| Title |
Transgenic (antisense OsDDM1) plant Replicate 2 vs. Control "Nipponbare" plant Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Young leaves of an antisense OsDDM1 plant
|
| Organism |
Oryza sativa |
| Characteristics |
genotype/variation: an antisense OsDDM1 line "1-17"
cultivar: Nipponbare
individual id: 1-17C
tissue: young leaves
|
| Treatment protocol |
Young leaves were sampled before the boot stage. Cut leaves were frozen using liquid nitrogen immediately after sampling.
|
| Growth protocol |
The transgenic line “1-17” harboring an antisense construct derived from a rice DDM1a EST clone, C30395_1A (the 5’ end sequence: AU062733), was produced as follows: A sequence of the EST clone (2 kb) was used for the antisense construction and inserted downstream of the 35S promoter of cauliflower mosaic virus in pBI101 binary vector in the antisense orientation with standard cloning techniques; The antisense construct was introduced into Agrobacterium tumefaciens (strain LBA4404); The transfected A. tumefaciens was allowed to infect primary callus derived from scutellum tissue and transgenic lines were generated according to an Agrobacterium-mediated transformation method of rice (Plant Molecular Biology Reporter 15 (1), 1997); The line 1-17 is a few generation descendant from a T0 plant [T0 plant: a plant regenerated from transformed calli]. Transgenic plants 1-17A and 1-17C are sibling individuals in the line 1-17.
Plants were raised in green house for about 2 months in a room of greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from young leaves by using Trizol (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
Low RNA inout Lineat Amplification/Labeling Lit (Agilent)
|
| |
|
| Channel 2 |
| Source name |
"Nipponbare" young leaves
|
| Organism |
Oryza sativa |
| Characteristics |
genotype/variation: cultiva "Nipponbare"
cultivar: Nipponbare
indivisual id: NB0-0
tissue: young leaves
|
| Treatment protocol |
Young leaves were sampled before the boot stage. Cut leaves were frozen using liquid nitrogen immediately after sampling.
|
| Growth protocol |
The transgenic line “1-17” harboring an antisense construct derived from a rice DDM1a EST clone, C30395_1A (the 5’ end sequence: AU062733), was produced as follows: A sequence of the EST clone (2 kb) was used for the antisense construction and inserted downstream of the 35S promoter of cauliflower mosaic virus in pBI101 binary vector in the antisense orientation with standard cloning techniques; The antisense construct was introduced into Agrobacterium tumefaciens (strain LBA4404); The transfected A. tumefaciens was allowed to infect primary callus derived from scutellum tissue and transgenic lines were generated according to an Agrobacterium-mediated transformation method of rice (Plant Molecular Biology Reporter 15 (1), 1997); The line 1-17 is a few generation descendant from a T0 plant [T0 plant: a plant regenerated from transformed calli]. Transgenic plants 1-17A and 1-17C are sibling individuals in the line 1-17.
Plants were raised in green house for about 2 months in a room of greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from young leaves by using Trizol (Invitrogen).
|
| Label |
Cy5
|
| Label protocol |
Low RNA inout Lineat Amplification/Labeling Lit (Agilent)
|
| |
|
| |
| Hybridization protocol |
Agilent protocol G4140-90040
|
| Scan protocol |
Agilent scanner model G2505B, software G2565BA
|
| Description |
Control biological replicate 2 vs. Transgenic biological replicate 2 (the dye-swap experiment)
|
| Data processing |
Data was analyzed by Fearure Extraction software (version 9.1, Agilent)
|
| |
|
| Submission date |
Aug 31, 2011 |
| Last update date |
Oct 02, 2012 |
| Contact name |
Naoki Kishimoto |
| Fax |
+81-29-838-7408
|
| Organization name |
National Institute of Agrobiological Sciences
|
| Department |
Agrogenomics Research Center
|
| Lab |
Plant Genome Engineering Research Unit
|
| Street address |
2-1-2 Kannondai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8602 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6864 |
| Series (1) |
| GSE31775 |
OsDDM1 regulated genes in rice: Control (wt: cultivar "Nipponbare") vs. Transgenic (antisense OsDDM1) |
|
