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Sample GSM409429 Query DataSets for GSM409429
Status Public on Jun 09, 2009
Title Nipponbare_young panicle 2cm, biological rep5
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 189.06 P 0.000662269
AFFX-BioB-M_at 215.905 P 4.42873e-05
AFFX-BioB-3_at 152.978 P 4.42873e-05
AFFX-BioC-5_at 451.332 P 5.16732e-05
AFFX-BioC-3_at 571.089 P 4.42873e-05
AFFX-BioDn-5_at 1032.59 P 4.42873e-05
AFFX-BioDn-3_at 2330.04 P 4.42873e-05
AFFX-CreX-5_at 5936.04 P 5.16732e-05
AFFX-CreX-3_at 7942.14 P 4.42873e-05
AFFX-DapX-5_at 37.8066 P 0.00141043
AFFX-DapX-M_at 164.76 P 0.000581214
AFFX-DapX-3_at 379.261 P 7.00668e-05
AFFX-LysX-5_at 18.4971 P 0.00124642
AFFX-LysX-M_at 46.1693 A 0.131361
AFFX-LysX-3_at 144.934 P 7.00668e-05
AFFX-PheX-5_at 28.1955 P 0.0032123
AFFX-PheX-M_at 45.5502 P 0.00401721
AFFX-PheX-3_at 63.0957 P 0.000340305
AFFX-ThrX-5_at 18.0991 A 0.287726
AFFX-ThrX-M_at 48.5145 P 0.000258358

Total number of rows: 57381

Table truncated, full table size 2179 Kbytes.




Supplementary file Size Download File type/resource
GSM409429.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM409429.CHP.gz 312.2 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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