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Sample GSM409430 Query DataSets for GSM409430
Status Public on Jun 09, 2009
Title 9311_young panicle 2cm, biological rep1
Sample type RNA
 
Source name young panicle 2cm
Organism Oryza sativa Indica Group
Characteristics tissue: young panicle
cultivar: 93-11
Extracted molecule total RNA
Extraction protocol total RNA was isolated and purified by RNeasy Plant Mini Kit (QIAGEN)
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol According to Affymetrix standard procedure, 10 micrograms of fragmented cRNA were hybridized to an array for 16-18 hours at 45┬░C with constant rotation at 60 rpm. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station.
Scan protocol GeneChips were scanned using Affymetrix GeneArray 3000 scanner.
Description Gene expression data from rice young panicle
Data processing The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method.
 
Submission date May 28, 2009
Last update date Jun 08, 2009
Contact name Nori Kurata
E-mail(s) nkurata@lab.nig.ac.jp
Phone +81-55-981-6808
Fax +81-55-981-6879
Organization name National Institute of Genetics
Lab Plant Genetics Lab.
Street address 1111 Yata
City Mishima
ZIP/Postal code 411-8540
Country Japan
 
Platform ID GPL2025
Series (1)
GSE16265 SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip

Data table header descriptions
ID_REF
VALUE Affymetrix GeneChip® Operating Software (GCOS, Version 1.3, 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 249.345 P 0.000662269
AFFX-BioB-M_at 290.046 P 4.42873e-05
AFFX-BioB-3_at 210.351 P 7.00668e-05
AFFX-BioC-5_at 666.055 P 5.16732e-05
AFFX-BioC-3_at 793.082 P 4.42873e-05
AFFX-BioDn-5_at 1324.16 P 4.42873e-05
AFFX-BioDn-3_at 3208.31 P 4.42873e-05
AFFX-CreX-5_at 7816.01 P 5.16732e-05
AFFX-CreX-3_at 9605.5 P 4.42873e-05
AFFX-DapX-5_at 331.594 P 5.16732e-05
AFFX-DapX-M_at 777.341 P 8.14279e-05
AFFX-DapX-3_at 1070.52 P 5.16732e-05
AFFX-LysX-5_at 52.9048 P 5.16732e-05
AFFX-LysX-M_at 88.7388 P 0.00933744
AFFX-LysX-3_at 254.031 P 5.16732e-05
AFFX-PheX-5_at 70.5804 P 0.00010954
AFFX-PheX-M_at 102.874 P 0.00010954
AFFX-PheX-3_at 129.154 P 8.14279e-05
AFFX-ThrX-5_at 82.8957 P 0.000126798
AFFX-ThrX-M_at 144.396 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2176 Kbytes.




Supplementary file Size Download File type/resource
GSM409430.CEL.gz 5.0 Mb (ftp)(http) CEL
GSM409430.CHP.gz 313.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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