|
| Status |
Public on Feb 15, 2013 |
| Title |
Rice ovule stage E4 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Rice ovule, mononuclear cell stage
|
| Organism |
Oryza sativa |
| Characteristics |
subspecies: japonica
cultivar: Nipponbare
developmental stage: mononuclear
tissue: ovule
|
| Treatment protocol |
Collected pistil samples were fixed in acetone overnight at 4 degree. Sections of 10 µm thickness were cut from paraffin-embedded samples and mounted on PEN membrane class slides (Life Technologies, Carlsbad, CA), then ovules were isolated using the Veritas Laser Microdissection System LCC1704 (Molecular Devices, Ontario, Canada).
|
| Growth protocol |
Wild-type rice plants (Oryza sativa L. cv. Nipponbare) were grown in paddy field under natural conditions at Mishima, Japan in the summer of 2009.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 50 - 150 pieces of microdissected ovules with a PicoPure™ RNA isolation kit (Life Technologies) following the manufacturer's recommendations. The qualities of the RNA samples were assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The RNA quantity was determined by the Quant-iT™ RiboGreen® RNA Assay Kit (Life Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled cRNA were prepared from total RNA using Quick Amp Labeling Kit (Agilent) in accordance with the manufacturer's protocol with slight modification. The cDNA synthesis reaction time was extended to 6 hrs.
|
| |
|
| Hybridization protocol |
Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 600 - 800 ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.
|
| Scan protocol |
Microarrays were scanned using Agilent DNA microarray scanner G2565BA according to manufacturer's instructions.
|
| Description |
Gene expression data in developing rice ovule
|
| Data processing |
Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent) using manufacturer's default extraction protocol named 'GE1-v5_95_Feb07'. The text data files produced by FeatureExtraction were introduced into GeneSpring 7.3.1, then the introduced signal intensities (gProcessedSignal) were scaled to the 75th percentile per chip (scaled the 75th percentile value was set to 10), and the lowest value of scaled signal intensity was set to 0.01.
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
Feb 15, 2013 |
| Contact name |
Nori Kurata |
| E-mail(s) |
nkurata@nig.ac.jp
|
| Phone |
+81-55-981-6808
|
| Organization name |
National Institute of Genetics
|
| Lab |
Plant genetics Lab.
|
| Street address |
1111 Yata
|
| City |
Mishima |
| State/province |
Shizuoka |
| ZIP/Postal code |
411-8540 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE35760 |
Transcriptomes of developing rice ovules |
|
