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Status |
Public on Jul 01, 2018 |
Title |
T1hAir_1 |
Sample type |
RNA |
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Source name |
Intercalary meristem at the 10~12 weeks stem in 1h Air, non-transgenic
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Organism |
Oryza sativa |
Characteristics |
cultivar: cv. Pin Gaew 56 (PG56) stress: Air time: 1h tissue: intercalary meristem
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Treatment protocol |
Deepwater rice stem sections were pre-incubated for 4 h and then further incubated complete submergence or air in continuous light for 24 h. Twenty stem sections were placed in an upright position in a 200-ml glass beaker which was then filled with glass beads to prevent the submerged sections from floating up. Each beaker containing the sections was lowered to the bottom of a plastic cylinder, filled to the 50-cm deep with distilled water. Stem sections were incubated under complete submergence or in air for 3 different times (0, 1 and 4 h).
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Growth protocol |
Seeds (Oriza sativa L. indica cultivar Pin Gaew 56) were geminated in darkness in petri dishes on moist filter paper at 30℃ for 72 h. Seedling were transplanted in plastic pots and grown in greenhouse. Twenty-cm-long stem sections containing the uppermost internode were excised from 10- to 12-week-old plants.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNAs were extracted using MiniBEST Plant RNA Extraction kit (TAKARA, Japan).
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Label |
Cy3
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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.
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Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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Description |
Intercalary meristem at the 10~12 weeks stem in 1h Air, non-transgenic, biological replicate 1
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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 |
Jun 28, 2017 |
Last update date |
Jul 01, 2018 |
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 |
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Platform ID |
GPL14568 |
Series (1) |
GSE100598 |
Transcriptome analysis of early submergence-responsive genes in deepwater rice |
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