|
| Status |
Public on Jul 22, 2009 |
| Title |
Root- +Fe-P biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Root segments derived from 11-d-old rice (Oryza sativa) seedlings under +Fe-P conditions
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: Root
|
| Treatment protocol |
For –Fe+P treatment, FeCl3 and citric acid were removed. For +Fe-P treatment, NaH2PO4 was removed. While for –Fe–P treatment, FeCl3, citric acid, and NaH2PO4 were removed.
|
| Growth protocol |
Rice seeds were germinated in distilled water for 2 d. After germination, 25 seedlings were transferred to a plastic net floating on the Yoshida nutrient solution (Yoshida et al., 1976).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAzol (Campro Scientific) and glass beads according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
The One-Cycle Target Labeling and Control Reagent kit (Affymetrix 900493) and the protocols optimized by Affymetrix were used to prepare biotinylated complementaryRNA (cRNA; from 5 mg of total RNA) for microarray hybridization (n = 2 per group).
|
| |
|
| Hybridization protocol |
Microarray analysis was carried out using an Affymetrix technology platform and Affymetrix GeneChip rice genome array. Briefly, fragmented cRNA was mixed with spiked controls and applied to Affymetrix Test chips, and good quality samples were then used to hybridize with the rice GeneChip. The hybridization, probe array washing and staining, and washing procedures were executed as described in the Affymetrix protocols.
|
| Scan protocol |
Probe arrays were scanned with a Hewlett-Packard Gene Array Scanner (Leiden Genome Technology Center).
|
| Description |
Gene expression data from 10-d-old rice (Oryza sativa) seedlings under +Fe-P conditions
|
| Data processing |
Data analysis was carried out using Avadis 4.3 (Strand Genomics) and Partek Genomics suite software, version 6.3. Raw intensity data were initially normalized using the MAS5 algorithm, which allowed probe identifier present calls to be determined.
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| |
|
| Submission date |
Jul 21, 2009 |
| Last update date |
Jul 21, 2009 |
| Contact name |
Luqing Zheng |
| E-mail(s) |
zluqing@gmail.com
|
| Organization name |
Colledge of Life Sciences, Zhejiang University
|
| Street address |
388 Yuhangtanghe Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE17245 |
Transcriptome analysis of iron and phosphorus interaction in rice seedlings |
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