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Sample GSM262011 Query DataSets for GSM262011
Status Public on Sep 22, 2008
Title Nipponbare, 2 days after mock-infection, biological replicate #2
Sample type RNA
 
Source name Oryza sativa uninfected roots, 2 days after mock-inoculation
Organism Oryza sativa Japonica Group
Characteristics synonym: Oryza sativa subsp. japonica
cultivar: Nipponbare
Age: 23 days
Treatment protocol Twenty one day-old seedlings were infected with 25 mg of preconditioned and pre-germinated Striga hermonthica seeds by aligning them along the roots. Control plants were treated in a similar manner (mock-inoculated).
Growth protocol Seedlings of the rice cultivars Nipponbare and IAC 165 (Oryza sativa subspecies japonica) were grown for three weeks in a controlled environment growth room under a 14 hour photoperiod with an irradiance of 400 μmol m-2 s-1, a daytime and night-time temperature of 27 oC and 23 oC respectively and 60% relative humidity.
Extracted molecule total RNA
Extraction protocol RNA was isolated using TRI reagent (Ambion) and then purified using an RNA purification column kit (Qiagen) according to manufacturer’s instructions.
Label biotin
Label protocol 3'IVT Affymetrix protocol using 5 ug total RNA
 
Hybridization protocol Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol Chips were scanned using an Affymetrix GeneChip scanner 3000 7G
Description Gene expression data from Oryza sativa (cultivar Nipponbare) uninfected roots, 2 days after mock-inoculation
Data processing Data were analysed using Affymetrix GCOS, with global scaling to a target of 100
 
Submission date Feb 04, 2008
Last update date Sep 22, 2008
Contact name Julie Scholes
Organization name University of Sheffield
Department Animal and Plant Sciences
Street address Western Bank
City Sheffield
ZIP/Postal code S10 2TN
Country United Kingdom
 
Platform ID GPL2025
Series (1)
GSE10373 Rice cultivars undergoing a susceptible and resistant interaction with the parasitic plant Striga hermonthica

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 5.8 A 0.368438
AFFX-BioB-M_at 145.5 P 0.00006
AFFX-BioB-3_at 120 P 0.000044
AFFX-BioC-5_at 433.4 P 0.000052
AFFX-BioC-3_at 299.6 P 0.000044
AFFX-BioDn-5_at 530.1 P 0.000044
AFFX-BioDn-3_at 1663.4 P 0.000044
AFFX-CreX-5_at 4455.1 P 0.000052
AFFX-CreX-3_at 5821.2 P 0.000044
AFFX-DapX-5_at 6.1 A 0.072682
AFFX-DapX-M_at 3.9 A 0.5
AFFX-DapX-3_at 0.6 A 0.891021
AFFX-LysX-5_at 0.4 A 0.891102
AFFX-LysX-M_at 3.7 A 0.631573
AFFX-LysX-3_at 2.9 A 0.574038
AFFX-PheX-5_at 0.6 A 0.945787
AFFX-PheX-M_at 1 A 0.804734
AFFX-PheX-3_at 1.1 A 0.824672
AFFX-ThrX-5_at 1 A 0.749204
AFFX-ThrX-M_at 2.3 A 0.425962

Total number of rows: 57381

Table truncated, full table size 1931 Kbytes.




Supplementary file Size Download File type/resource
GSM262011.CEL.gz 8.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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