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Sample GSM304653 Query DataSets for GSM304653
Status Public on Jul 31, 2008
Title Mutant stable line
Sample type RNA
Source name gamma-irradiated rice mutant (semidwarf mutant)- Over 10 generations of self-pollination
Organism Oryza sativa
Characteristics Tissue:six whole seedlings with 12 days
Plant: Oryza sativa L. ssp japonica (cv. Estrela A)
gamma-irradiated rice mutant (semidwarf mutant)- Over 10 generations of self-pollination
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 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 gamma-irradiated rice mutant (semidwarf mutant)- Over 10 generations of self-pollination, cv. Estrela A
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
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

Data table header descriptions
VALUE gamma-irradiated rice mutant (semidwarf mutant)- Over 10 generations of self-pollination

Data table
AFFX-BioB-5_at 8.15
AFFX-BioB-M_at 7.63
AFFX-BioB-3_at 7.86
AFFX-BioC-5_at 9.00
AFFX-BioC-3_at 9.12
AFFX-BioDn-5_at 10.58
AFFX-BioDn-3_at 11.86
AFFX-CreX-5_at 13.00
AFFX-CreX-3_at 13.28
AFFX-DapX-5_at 9.44
AFFX-DapX-M_at 10.19
AFFX-DapX-3_at 11.04
AFFX-LysX-5_at 6.51
AFFX-LysX-M_at 6.96
AFFX-LysX-3_at 8.51
AFFX-PheX-5_at 7.71
AFFX-PheX-M_at 7.75
AFFX-PheX-3_at 8.21
AFFX-ThrX-5_at 8.09
AFFX-ThrX-M_at 8.31

Total number of rows: 57381

Table truncated, full table size 1349 Kbytes.

Supplementary file Size Download File type/resource
GSM304653.CEL.gz 5.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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