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Sample GSM409433 Query DataSets for GSM409433
Status Public on Jun 09, 2009
Title 9311_young panicle 2cm, biological rep4
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 242.763 P 0.000662269
AFFX-BioB-M_at 194.465 P 4.42873e-05
AFFX-BioB-3_at 143.726 P 7.00668e-05
AFFX-BioC-5_at 434.203 P 5.16732e-05
AFFX-BioC-3_at 592.968 P 4.42873e-05
AFFX-BioDn-5_at 997.626 P 4.42873e-05
AFFX-BioDn-3_at 2346.21 P 5.16732e-05
AFFX-CreX-5_at 6124.39 P 5.16732e-05
AFFX-CreX-3_at 7370.14 P 4.42873e-05
AFFX-DapX-5_at 188.147 P 4.42873e-05
AFFX-DapX-M_at 372.338 P 0.000169227
AFFX-DapX-3_at 422.027 P 5.16732e-05
AFFX-LysX-5_at 14.3957 P 0.0103112
AFFX-LysX-M_at 43.3937 A 0.0676785
AFFX-LysX-3_at 106.068 P 7.00668e-05
AFFX-PheX-5_at 30.6832 P 0.000224668
AFFX-PheX-M_at 40.5191 P 0.00255552
AFFX-PheX-3_at 41.7249 P 7.00668e-05
AFFX-ThrX-5_at 51.1283 P 0.00110197
AFFX-ThrX-M_at 69.9867 P 9.4506e-05

Total number of rows: 57381

Table truncated, full table size 2176 Kbytes.




Supplementary file Size Download File type/resource
GSM409433.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM409433.CHP.gz 313.3 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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