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Sample GSM409421 Query DataSets for GSM409421
Status Public on Jun 09, 2009
Title Nipponbare_young panicle 2cm, biological rep1
Sample type RNA
Source name young panicle 2cm
Organism Oryza sativa Japonica Group
Characteristics tissue: young panicle
cultivar: Nipponbare
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
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
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
AFFX-BioB-5_at 196.731 P 0.00141043
AFFX-BioB-M_at 182.447 P 4.42873e-05
AFFX-BioB-3_at 153.073 P 5.16732e-05
AFFX-BioC-5_at 489.434 P 5.16732e-05
AFFX-BioC-3_at 557.077 P 5.16732e-05
AFFX-BioDn-5_at 998.523 P 4.42873e-05
AFFX-BioDn-3_at 2544.54 P 5.16732e-05
AFFX-CreX-5_at 5961.94 P 5.16732e-05
AFFX-CreX-3_at 7905.65 P 4.42873e-05
AFFX-DapX-5_at 298.011 P 4.42873e-05
AFFX-DapX-M_at 677.406 P 8.14279e-05
AFFX-DapX-3_at 1059.16 P 5.16732e-05
AFFX-LysX-5_at 58.1027 P 0.000126798
AFFX-LysX-M_at 79.0212 P 0.0429619
AFFX-LysX-3_at 222.563 P 5.16732e-05
AFFX-PheX-5_at 62.5295 P 9.4506e-05
AFFX-PheX-M_at 79.7143 P 0.000581214
AFFX-PheX-3_at 90.7656 P 4.42873e-05
AFFX-ThrX-5_at 93.5939 P 0.000146581
AFFX-ThrX-M_at 152.906 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2180 Kbytes.

Supplementary file Size Download File type/resource
GSM409421.CEL.gz 5.1 Mb (ftp)(http) CEL
GSM409421.CHP.gz 309.7 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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