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Sample GSM275416 Query DataSets for GSM275416
Status Public on Mar 19, 2008
Title Azucena root tip_Before the wax layer_Rep3
Sample type RNA
 
Source name Azucena root tip_Before 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. RNA was harvested from root tips which were 5-10 mm above the wax layer. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep3.
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) which were above the 60% wax layer, 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 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 116.8 P
AFFX-BioB-M_at 159.6 P
AFFX-BioB-3_at 119.5 P
AFFX-BioC-5_at 330.4 P
AFFX-BioC-3_at 308.9 P
AFFX-BioDn-5_at 642.6 P
AFFX-BioDn-3_at 1220.9 P
AFFX-CreX-5_at 3074.3 P
AFFX-CreX-3_at 4216.6 P
AFFX-DapX-5_at 194.4 P
AFFX-DapX-M_at 403.6 P
AFFX-DapX-3_at 814.3 P
AFFX-LysX-5_at 36.2 P
AFFX-LysX-M_at 62.1 P
AFFX-LysX-3_at 95.1 P
AFFX-PheX-5_at 69.4 P
AFFX-PheX-M_at 83.1 P
AFFX-PheX-3_at 98.6 P
AFFX-ThrX-5_at 60.3 P
AFFX-ThrX-M_at 112.1 P

Total number of rows: 57381

Table truncated, full table size 1428 Kbytes.




Supplementary file Size Download File type/resource
GSM275416.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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