|
| Status |
Public on Apr 05, 2012 |
| Title |
A-OsMADS29 (line2) rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Nucellar projection cells, A-OsMADS29 (line2),3 DAF, replicate 1
|
| Organism |
Oryza sativa |
| Characteristics |
genetic background: ZH11
genotype: OsMADS29 mutant
source tissue: seed
cell type: Nucellar projection cells
age: 3 DAF
|
| Growth protocol |
ZH11 and A-OsMADS29 (line2 and line14) were growth in the same conditon.The rice seeds were germinated in sterilized water and then grown in pots in a phytotron with a 12-h light (26℃) / 12-h dark (18℃) cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nucellar projection cells of seeds at 3 DAF were isolated using a Veritas Microdissection System (Arcturus/Molecular Devices).The RNA was extracted with the PicoPure RNA Isolation Kit (Arcturus/Molecular Devices) and amplified using a TargetAmp 2-round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnologies) following the manufacturer's recommendations. RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression 4*44K Microarrays for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.
|
| Description |
Gene expression in nucellar projection of 3 DAF A-OsMADS29 (line2) seed
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 015241_D_F_20081112) to obtain background subtracted and spatially detrended Processed Signal intensities.
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| |
|
| Submission date |
Sep 06, 2011 |
| Last update date |
Apr 05, 2012 |
| Contact name |
linlin yin |
| Organization name |
SIPPE
|
| Street address |
300 fenglin road
|
| City |
shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE31893 |
OsMADS29 regulates the degradation of the nucellus and the nucellar projection during rice seed development |
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