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Sample GSM240999 Query DataSets for GSM240999
Status Public on Nov 02, 2007
Title gif1 7 DAF, biological replicate 3
Sample type RNA
 
Source name Oryza sativa mutant_gif1 Caryopsis, 7 DAF
Organism Oryza sativa
Characteristics Genotype: gif1, mutant, Age: 7 DAF, Tissue: caryopsis
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from caryopsis using the Trizol method (Invitrogen) and purified with RNeasy MiniKit (Qiagen). cDNA was synthesized and purified with one-cycle cDNA Synthesis Kit (Affymetrix) and GeneChip Sample Cleanup Module (Affymetrix), respectively.
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit and Genechip Sample Cleanup Module (Affymetrix)
 
Hybridization protocol Affymetrix standard protocol
Scan protocol Affymetrix standard protocol
Description Gene expression data of mutant gif1 caryopsis, 7 DAF
Data processing The data were analyzed with Affymetrix GeneChip® Operating Software (GCOS, Version 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Nov 01, 2007
Last update date Aug 14, 2011
Contact name Li Qun
E-mail(s) qli@sibs.ac.cn
Phone +86 21 54924122
Organization name Institute of plant physiology & ecology, SIBS, CAS
Department National Key Laboratory of Plant Molecular Genetics
Street address 300 Fenglin Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL2025
Series (1)
GSE9498 Global gene expression profiles of Oryza sativa wild type Zhonghua11 and mutant gif1 in filling stage

Data table header descriptions
ID_REF Affymetrix Probe Set ID
VALUE Affymetrix GeneChip® Operating Software (GCOS, Version 1.4, Affymetrix) calculated Signal intensity
ABS_CALL The call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
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 682.5 P 0.000081
AFFX-BioB-M_at 908 P 0.000044
AFFX-BioB-3_at 675.5 P 0.000052
AFFX-BioC-5_at 851.2 P 0.000052
AFFX-BioC-3_at 830.4 P 0.000044
AFFX-BioDn-5_at 7072 P 0.000044
AFFX-BioDn-3_at 12277.4 P 0.000044
AFFX-CreX-5_at 29381.4 P 0.000044
AFFX-CreX-3_at 37405.6 P 0.000044
AFFX-DapX-5_at 1355.6 P 0.00007
AFFX-DapX-M_at 2742.5 P 0.000052
AFFX-DapX-3_at 3778.1 P 0.000044
AFFX-LysX-5_at 154 P 0.000147
AFFX-LysX-M_at 159.9 A 0.0727
AFFX-LysX-3_at 420.2 P 0.00007
AFFX-PheX-5_at 255.6 P 0.000581
AFFX-PheX-M_at 214.7 P 0.000662
AFFX-PheX-3_at 212 P 0.000195
AFFX-ThrX-5_at 320.2 P 0.00007
AFFX-ThrX-M_at 525.1 P 0.000044

Total number of rows: 57381

Table truncated, full table size 1961 Kbytes.




Supplementary file Size Download File type/resource
GSM240999.CEL.gz 7.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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