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Sample GSM149409 Query DataSets for GSM149409
Status Public on Dec 11, 2006
Title Rice Azucena 0ppm Arsenate (Control) Rep3
Sample type RNA
 
Source name Rice Hydroponic Roots 1 Week Old
Organism Oryza sativa
Characteristics Rice variety Azucena, 1 week in hydroponics, whole root system
Treatment protocol Germinated seedlings were grown for 1 week in hydroponics with 0ppm arsenate under 12 hr of light as described in Dasgupta T, Hossain SA, Meharg AA and Price AH. (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytologist 163: 45-49
Growth protocol Dasgupta T, Hossain SA, Meharg AA and Price AH. (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytologist 163: 45-49
Extracted molecule total RNA
Extraction protocol 100 mg of root material was pooled from four separate plants and RNA was extracted using the TRIzol method (Invitrogen) followed by further purification and DNase treatment using the RNeasy clean up kit (Qiagen).
Label biotin
Label protocol RNA was processed for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. Briefly, 5 ug of total RNA was used in the one-cycle cDNA synthesis reaction. After the generation of double stranded cDNA an in vitro transcription reaction was performed to generate biotinylated cRNA. (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Hybridisation, washing and staining procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.
Scan protocol Scanning procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.
Description Gene expression data from rice roots (variety Azucena) grown in hydroponics for one week with 0ppm arsenate, rep3
Data processing The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Dec 11, 2006
Last update date Dec 11, 2006
Contact name Gareth Norton
E-mail(s) g.norton@abdn.ac.uk
Organization name University of Aberdeen
Department Plant and Soil Science
Lab Rice genetics
Street address St Machar drive
City Aberdeen
ZIP/Postal code AB24 3UU
Country United Kingdom
 
Platform ID GPL2025
Series (1)
GSE4471 Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 93.9 P 0.000509
AFFX-BioB-M_at 107.2 P 0.000052
AFFX-BioB-3_at 100.8 P 0.000044
AFFX-BioC-5_at 310.2 P 0.000044
AFFX-BioC-3_at 257.8 P 0.000044
AFFX-BioDn-5_at 464.3 P 0.000044
AFFX-BioDn-3_at 1070 P 0.000044
AFFX-CreX-5_at 2980.6 P 0.000044
AFFX-CreX-3_at 3682.2 P 0.000044
AFFX-DapX-5_at 94.9 P 0.00007
AFFX-DapX-M_at 239.6 P 0.000095
AFFX-DapX-3_at 485 P 0.00007
AFFX-LysX-5_at 22.6 P 0.00039
AFFX-LysX-M_at 31.6 A 0.095667
AFFX-LysX-3_at 63.9 P 0.00011
AFFX-PheX-5_at 29.6 P 0.000258
AFFX-PheX-M_at 36.6 P 0.00007
AFFX-PheX-3_at 58.2 P 0.000297
AFFX-ThrX-5_at 30.4 P 0.000662
AFFX-ThrX-M_at 58.4 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1925 Kbytes.




Supplementary file Size Download File type/resource
GSM149409.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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