|
| Status |
Public on Dec 01, 2010 |
| Title |
FR13A_control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
FR13A, control, replicate1
|
| Organism |
Oryza sativa |
| Characteristics |
developmental stage: 14 d-old-seedlings
tissue: leaf
cultivar: FR13A
|
| Treatment protocol |
Fourteen-day-old seedlings were submerged in a 300 L plastic tank with water 70 cm deep for 3 d. The distance from the tip of the shoot to the water surface was 52.7 ±2.3 and 45.9 ± 2.9 cm per seedling at the start of complete submergence for FR13A and Goda Heenati, respectively. Controls were set out in a plastic tank without water.Daily air temperature ranged between 24℃ and 28℃ and the water temperature range was 22–25℃ during the experimental period.
|
| Growth protocol |
Approximately 60 pre-germinated seeds were sown in 0.50 L plastic pots filled with paddy fields soil. The plants were grown without fertilizer in a glasshouse with an air temperature range of 24-28℃under natural daylight, and thinned to 20 plants per pot.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaves of approximately 20 plants for each genotype and treatment were harvested from various pots and pooled to make one sample for RNA extraction. Total RNAs were extracted using Trizol (Invitrogen Life Technologies), and further purified with Qiagen Rneasy mini kit (Qiagen) following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 2 μg total RNA using the Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
Labeled cRNA of 1 µg was used for hybridization in a rice 4×44K oligo microarray (Agilent Technologies). The hybridization was performed at 65℃for 17 h in a rotating Agilent hybridization oven (G2545A).
|
| Scan protocol |
microarray slides were scanned using a DNA microarray scanner (G2505C, Agilent) with one color scan setting (Scan resolution 5 um, PMT is set to 100% and 10%).
|
| Description |
Gene expression levels in non-submerged FR13A
|
| Data processing |
Signal intensities were extracted by Feature Extraction software (version 10.5.1.1, Agilent Technologies) at the default settings. Data were quantile normalized across all samples with the GeneSpring GX 10.0.
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| |
|
| Submission date |
Aug 11, 2010 |
| Last update date |
Aug 11, 2010 |
| Contact name |
Huaiyang Xiong |
| E-mail(s) |
xionghy1971@yahoo.com.cn
|
| Organization name |
Wuhan University
|
| Street address |
Eighty one road
|
| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE23574 |
Comparative Transcriptional Profiling of Two Rice Genotypes, FR13A and Goda Heenati, Under Submergence Stress |
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