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Sample GSM275408 Query DataSets for GSM275408
Status Public on Mar 19, 2008
Title Bala root tip_At the wax layer_rep1
Sample type RNA
 
Source name Bala root tip_At the wax layer
Organism Oryza sativa
Characteristics Rice variety Bala, 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 Bala) 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 170.8 P
AFFX-BioB-M_at 251.1 P
AFFX-BioB-3_at 162.3 P
AFFX-BioC-5_at 556.9 P
AFFX-BioC-3_at 478.7 P
AFFX-BioDn-5_at 938.6 P
AFFX-BioDn-3_at 1827.7 P
AFFX-CreX-5_at 4593.5 P
AFFX-CreX-3_at 5918.5 P
AFFX-DapX-5_at 183.9 P
AFFX-DapX-M_at 336.6 P
AFFX-DapX-3_at 672.5 P
AFFX-LysX-5_at 32 P
AFFX-LysX-M_at 37.8 P
AFFX-LysX-3_at 71.4 P
AFFX-PheX-5_at 46.8 P
AFFX-PheX-M_at 50.2 P
AFFX-PheX-3_at 79.2 P
AFFX-ThrX-5_at 55.5 P
AFFX-ThrX-M_at 86.4 P

Total number of rows: 57381

Table truncated, full table size 1427 Kbytes.




Supplementary file Size Download File type/resource
GSM275408.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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