|
| Status |
Public on Jul 28, 2016 |
| Title |
RegCal_2 |
| Sample type |
RNA |
| |
|
| Source name |
The regenerating calli were induced from calli for 2 weeks on a MS16 medium and collected when turned green.
|
| Organism |
Oryza sativa |
| Characteristics |
self-fertile and virulent on host plants: Oryza sativa L. cv. Dongjin
cultivar: Oryza sativa L. cv. Dongjin
|
| Treatment protocol |
The calli were induced from seeds on 2N6 medium at 37°C for 4 weeks. The regenerating calli were induced from calli for 2 weeks on a MS16 medium and collected when turned green. The seeds were germinated on water-soaked filter paper for 4 days in a dark chamber. Leaves and roots were harvested separately 14 days after sowing in soil. A flower sample was harvested at exact stages following recommendations from previous research. The flowers before pollination were prepared just prior to the opening of the spikelet, and the flowers after pollination were collected followed by anthesis, respectively. The flower before pollination (FBP) was collected prior to the opening of the spikelet, and its pistil length was in the range of 0.5 to 1.5 mm. The flower after pollination (FAP) was collected after the anthesis and maximum opening of the florets.
|
| Growth protocol |
All seven tissues in this study were prepared from Oryza sativa L. cv. Dongjin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TriReagent (Molecular Research Center, Inc.).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
The regenerating calli were induced from calli for 2 weeks on a MS16 medium and collected when turned green.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
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| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
Jul 28, 2016 |
| Contact name |
Yeon-Ki Kim |
| E-mail(s) |
kim750a11@gmail.com
|
| Phone |
82-31-321-6351
|
| Organization name |
GreenGene Biotech Inc.
|
| Department |
GreenGene Biotech Inc.
|
| Lab |
Genomics & Genetics Ins.
|
| Street address |
38-2 Namdong
|
| City |
Yongin |
| State/province |
Kyonggido |
| ZIP/Postal code |
449-728 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL22243 |
| Series (1) |
| GSE84903 |
Analysis of representative organ specific genes and promoters of rice using 3’ ORF oriented long oligomer microarray |
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