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Sample GSM275405 Query DataSets for GSM275405
Status Public on Mar 19, 2008
Title Azucena root tip_At the wax layer_rep1
Sample type RNA
 
Source name Azucena root tip_At the wax layer
Organism Oryza sativa
Characteristics Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep1.
Biomaterial provider University of Aberdeen, Rice molecular genetic group
Treatment protocol N/A
Growth protocol Plants were grown in a controlled environment room with a 12 hour day and night, with a day temperature of 30oC and a night temperature of 24oC with 300 ┬Ámol m-2 s-1 PAR.
Extracted molecule total RNA
Extraction protocol A total of 100 mg of root tips (last 5 mm of the root) was harvested and RNA 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 root tips (variety Azucena) in contact with a 60% wax layer, rep1
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 Mar 17, 2008
Last update date Mar 18, 2008
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)
GSE10857 Gene expression of rice root tips before, at and buckled by a hard layer in two rice varieties

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 174.8 P
AFFX-BioB-M_at 217.9 P
AFFX-BioB-3_at 178.4 P
AFFX-BioC-5_at 550 P
AFFX-BioC-3_at 483 P
AFFX-BioDn-5_at 799.1 P
AFFX-BioDn-3_at 1838.9 P
AFFX-CreX-5_at 4356.8 P
AFFX-CreX-3_at 6171.4 P
AFFX-DapX-5_at 253.1 P
AFFX-DapX-M_at 616.2 P
AFFX-DapX-3_at 1361.4 P
AFFX-LysX-5_at 44.7 P
AFFX-LysX-M_at 88.3 P
AFFX-LysX-3_at 201.6 P
AFFX-PheX-5_at 102.7 P
AFFX-PheX-M_at 127.8 P
AFFX-PheX-3_at 200.5 P
AFFX-ThrX-5_at 95.5 P
AFFX-ThrX-M_at 239.7 P

Total number of rows: 57381

Table truncated, full table size 1430 Kbytes.




Supplementary file Size Download File type/resource
GSM275405.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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