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Sample GSM409428 Query DataSets for GSM409428
Status Public on Jun 09, 2009
Title Nipponbare_young panicle 2cm, biological rep4
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
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 219.62 P 0.000340305
AFFX-BioB-M_at 207.888 P 4.42873e-05
AFFX-BioB-3_at 152.227 P 4.42246e-05
AFFX-BioC-5_at 447.739 P 4.42873e-05
AFFX-BioC-3_at 538.982 P 4.42873e-05
AFFX-BioDn-5_at 1129.9 P 4.42873e-05
AFFX-BioDn-3_at 2428.74 P 5.16732e-05
AFFX-CreX-5_at 6610.85 P 5.16732e-05
AFFX-CreX-3_at 8144.94 P 4.42873e-05
AFFX-DapX-5_at 353.323 P 4.42873e-05
AFFX-DapX-M_at 692.32 P 7.00668e-05
AFFX-DapX-3_at 833.501 P 5.16732e-05
AFFX-LysX-5_at 45.0862 P 4.42246e-05
AFFX-LysX-M_at 80.688 P 0.00499819
AFFX-LysX-3_at 196.184 P 5.16732e-05
AFFX-PheX-5_at 87.3632 P 8.14279e-05
AFFX-PheX-M_at 70.9165 P 8.14279e-05
AFFX-PheX-3_at 114.369 P 5.16014e-05
AFFX-ThrX-5_at 91.9267 P 0.000258358
AFFX-ThrX-M_at 128.814 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2186 Kbytes.




Supplementary file Size Download File type/resource
GSM409428.CEL.gz 5.0 Mb (ftp)(http) CEL
GSM409428.CHP.gz 309.8 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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