|
| Status |
Public on Oct 21, 2015 |
| Title |
Developing seeds of WT Replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Zhonghua 11 Developing seeds
|
| Organism |
Oryza sativa |
| Characteristics |
genotype/variation: Zhonghua 11 (wild type)
tissue: developing seeds
development stage: 10th day after fertilization
|
| Growth protocol |
The wild-type rice (Oryza sativa L.) was the japonica variety, Zhonghua 11. The wild-type and transgenic plants were grown in a field station in Beijing, China, from May through October, 2012.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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.
|
| |
|
| Hybridization protocol |
1.65ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression Microarray（4x44K） 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 (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
|
| |
|
| Submission date |
Oct 20, 2015 |
| Last update date |
Oct 21, 2015 |
| Contact name |
Congming Lu |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Botany, CAS
|
| Department |
The Key Laboratory of Photobiology, CAS
|
| Lab |
Lu Congming
|
| Street address |
Haidian Xiangshan Nanxincun 20#
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE74204 |
Enhanced sucrose loading improves rice yield by increasing grain size |
|
