|
| Status |
Public on Jun 29, 2022 |
| Title |
ZH11, primordia at the In2–In3 stages, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
panilce primordia at the In2–In3 stages,replicate 2
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: panicle primordia
Stage: In2–In3 stages
line: wild type ZH11
|
| Treatment protocol |
There is no treatment.
|
| Growth protocol |
All the plants grown in a paddy field in Shanghai (June–October), China.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by RNA QUEOUS KIT(Ambion-1912) following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the LowInput Quick-Amp Labeling Kit，one-color(24×) (Agilent,5190-2305) according to the manufacturer's instructions, followed by RNeasy® Mini Kit (QIAGEN, 74106). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
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| |
|
| Hybridization protocol |
0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent rice Gene Expression（4*44K）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 and profile AgilentHD_GX_1Color for 4x44K microarrays.
|
| Description |
Gene expression of panicle primordia in wild type ZH11
|
| 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 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
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| |
|
| Submission date |
Mar 31, 2022 |
| Last update date |
Jun 29, 2022 |
| Contact name |
Yan-Jie Zhang |
| E-mail(s) |
ljj307@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Street address |
800 Dongchuan RD. Minhang District
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE199873 |
DEG of panicle primordia in ZH11 and OsGATA6-AM lines at the In2 and In3 stages |
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