|
| Status |
Public on Dec 17, 2013 |
| Title |
Third leaf primordium-rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Third leaf primordium-rep 3
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Zhonghua 15
organ: leaf
|
| Growth protocol |
Rice (O. sativa L. ssp. japonica cv. Zhonghua 15) seeds were soaked in water at 30oC for about a week. Then seedlings were transplanted in plastic pots and cultured at 30±2oC under 11 hours day/13 hours night cycle in growth chamber, or transplanted into the experimental field in growing season.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol Reagent from Invitrogen Life Technologies.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol by amplifying and labeling 50-300ng total RNA with Two-Cycle Eukaryotic Target Labeling Assay kit.
|
| |
|
| Hybridization protocol |
The resulting cRNA was used for hybridization in the Affymetrix® Hybridization Oven 640 according to manufacturer’s instruction. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000. GeneChip Operating software (GCOS 1.4) were adopted for transforming pixels to intensities .
|
| Description |
Dissected from rice embryos after the seeds were soaked in water for 2-3 days
|
| Data processing |
Raw data was processed by an adjustment method to remove the bias raising from the two-cycle RNA linear amplification at probe level(Wang F, Chen R, Ji D, Bai S, Qian M, Deng M. 2013. Adjustment method for microarray data generated using two-cycle RNA labeling protocol. BMC Genomics 14(1): 31.), and then RMA was used for background correction, normalization and summary in Bioconductor.
|
| |
|
| Submission date |
Dec 16, 2013 |
| Last update date |
Aug 12, 2014 |
| Contact name |
Rui Chen |
| E-mail(s) |
[email protected]
|
| Phone |
+86-010-62755870
|
| Organization name |
Peking University
|
| Department |
College of Life Sciences
|
| Lab |
Bai SN's Lab
|
| Street address |
5 Yiheyuan Road, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE53347 |
A Gene Expression Profiling of Early Rice Stamen Development that Reveals Inhibition of Photosynthetic Genes by OsMADS58 |
|
