|
| Status |
Public on Jul 31, 2008 |
| Title |
Unstable transgenic line (1) |
| Sample type |
RNA |
| |
|
| Source name |
T1 generation of an Agrobacterium tumefaciens transformed line (AtRD29A driven BCBF1 gene, hpt gene)
|
| Organism |
Oryza sativa |
| Characteristics |
Tissue:six whole seedlings with 12 days
Plant: Oryza sativa L. ssp japonica (cv. Nipponbare)
T1 generation of an Agrobacterium tumefaciens transformed line (AtRD29A driven BCBF1 gene, hpt gene)
|
| Treatment protocol |
Seeds were manually peeled and immersed for 30 min at 50°C in 0.1% Benlate (fungicide). After washing in distilled sterilized water, seeds were surface-disinfected with 70% (vol/vol) ethanol for 1 min and then with a solution of 2% sodium hypochloride with traces of Tween 20, for 30 min, at room temperature. After thorough washing with distilled sterile water seeds were kept overnight in the final wash.
|
| Growth protocol |
Treated seeds were then soaked in Yoshida’s medium, supplemented with 30 mg/liter of hygromicin B, for germination in the dark for 2 days at 28°C. Seedlings were further grown at 28°C for 10 days under a 12-h photoperiod regime. Twelve-day-old seedlings were frozen in liquid nitrogen and kept at -80°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions. Total RNA was kept at -80°C and sent to the Affymetrix core facility (Instituto Gulbenkian de Ciência, Oeiras, Portugal).
|
| Label |
Biotin
|
| Label protocol |
Through synthesis of cRNA with incorporation of biotinylated ribonucleotide analogs.
|
| |
|
| Hybridization protocol |
Hybridization to the GeneChip Rice Genome Array (Affymetrix). This array contains probes to query 51,279 transcripts representing two rice subspecies (48,564 japonica transcripts and 1,260 transcripts of indica subspecies).
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner.
|
| Description |
T1 generation of an Agrobacterium tumefaciens transformed line (AtRD29A driven BCBF1 gene, hpt gene), cv. Nipponbare
|
| Data processing |
Microarrays data analysis was performed with Partek Genomics Suite software. Affymetrix CEL files were imported by using the Robust Multichip Average method, which involves four steps: background correction of the perfect match values, quintile normalization across all of the chips in the experiment, Log2 transformation, and median polish summarization. The logged data were used for hierarchical cluster analysis and statistical analysis.
|
| |
|
| Submission date |
Jul 10, 2008 |
| Last update date |
Jul 10, 2008 |
| Contact name |
Rita Maria Batista |
| E-mail(s) |
[email protected]
|
| Phone |
+351 217519311
|
| Organization name |
Instituto Nacional de Saude Dr. Ricardo Jorge
|
| Department |
Food safety and nutrition
|
| Street address |
Av Padre Cruz
|
| City |
Lisbon |
| ZIP/Postal code |
1649-016 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE12069 |
Mycroarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion |
|
