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Sample GSM262018 Query DataSets for GSM262018
Status Public on Sep 22, 2008
Title Nipponbare, 11 days after mock-infection, biological replicate #1
Sample type RNA
Source name Oryza sativa uninfected roots, 11 days after mock-inoculation
Organism Oryza sativa Japonica Group
Characteristics synonym: Oryza sativa subsp. japonica
cultivar: Nipponbare
Age: 32 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, 11 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
VALUE MAS5.0 signal intensity

Data table
AFFX-BioB-5_at 9.5 A 0.340661
AFFX-BioB-M_at 167.6 P 0.00007
AFFX-BioB-3_at 119.2 P 0.000044
AFFX-BioC-5_at 480.7 P 0.000052
AFFX-BioC-3_at 338.3 P 0.000044
AFFX-BioDn-5_at 518.1 P 0.000044
AFFX-BioDn-3_at 1955.9 P 0.000052
AFFX-CreX-5_at 4790.9 P 0.000044
AFFX-CreX-3_at 6570.4 P 0.000044
AFFX-DapX-5_at 4.6 A 0.340661
AFFX-DapX-M_at 2.2 A 0.455413
AFFX-DapX-3_at 11.9 A 0.239063
AFFX-LysX-5_at 3.3 A 0.185131
AFFX-LysX-M_at 13.4 A 0.39692
AFFX-LysX-3_at 1.6 A 0.51489
AFFX-PheX-5_at 1.1 A 0.891041
AFFX-PheX-M_at 7.1 A 0.425962
AFFX-PheX-3_at 2.4 A 0.772364
AFFX-ThrX-5_at 1.1 A 0.824672
AFFX-ThrX-M_at 1.2 A 0.574038

Total number of rows: 57381

Table truncated, full table size 1931 Kbytes.

Supplementary file Size Download File type/resource
GSM262018.CEL.gz 8.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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