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Sample GSM304390 Query DataSets for GSM304390
Status Public on Jul 31, 2008
Title Stable transgenic rice line
Sample type RNA
 
Source name T3 generation of a transgenic line expressing a single-chain Fv antibody (ScFvT84.66) against a carcinoembryonic antigen (CEA)
Organism Oryza sativa
Characteristics Tissue:six whole seedlings with 12 days
Plant: Oryza sativa L. ssp japonica (cv. Bengal)
T3 generation of a transgenic line expressing a single-chain Fv antibody (ScFvT84.66) against a carcinoembryonic antigen (CEA)
Biomaterial provider Dr. Eva Stöger (Institute of Molecular Biotechnology, Aachen University, Aachen, Germany)
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 T3 generation of a transgenic line expressing a single-chain Fv antibody (ScFvT84.66) against a carcinoembryonic antigen (CEA).
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 09, 2008
Last update date Jul 10, 2008
Contact name Rita Maria Batista
E-mail(s) rita.batista@insa.min-saude.pt
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
ID_REF
VALUE T3 generation of a transgenic line expressing a single-chain Fv antibody (ScFvT84.66) against a carcinoembryonic antigen (CEA)

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.55
AFFX-BioB-M_at 8.22
AFFX-BioB-3_at 8.36
AFFX-BioC-5_at 9.61
AFFX-BioC-3_at 9.55
AFFX-BioDn-5_at 11.15
AFFX-BioDn-3_at 12.20
AFFX-CreX-5_at 13.40
AFFX-CreX-3_at 13.70
AFFX-DapX-5_at 9.30
AFFX-DapX-M_at 9.97
AFFX-DapX-3_at 10.97
AFFX-LysX-5_at 6.74
AFFX-LysX-M_at 6.81
AFFX-LysX-3_at 8.45
AFFX-PheX-5_at 7.74
AFFX-PheX-M_at 7.75
AFFX-PheX-3_at 8.11
AFFX-ThrX-5_at 7.99
AFFX-ThrX-M_at 8.33

Total number of rows: 57381

Table truncated, full table size 1349 Kbytes.




Supplementary file Size Download File type/resource
GSM304390.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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