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Sample GSM262013 Query DataSets for GSM262013
Status Public on Sep 22, 2008
Title Nipponbare, 2 days after infection with S. hermonthica, biological replicate #2
Sample type RNA
Source name Oryza sativa roots infected with Striga hermonthica at 2 days post-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) roots infected with Striga hermonthica at 2 days post-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 10.5 A 0.089478
AFFX-BioB-M_at 165.8 P 0.000052
AFFX-BioB-3_at 123.1 P 0.000052
AFFX-BioC-5_at 485.3 P 0.000044
AFFX-BioC-3_at 369.1 P 0.000044
AFFX-BioDn-5_at 598.1 P 0.000044
AFFX-BioDn-3_at 2039.4 P 0.000044
AFFX-CreX-5_at 5041.2 P 0.000052
AFFX-CreX-3_at 6571 P 0.000044
AFFX-DapX-5_at 3.8 A 0.185131
AFFX-DapX-M_at 3.5 A 0.48511
AFFX-DapX-3_at 5.5 A 0.340661
AFFX-LysX-5_at 3.9 A 0.5
AFFX-LysX-M_at 9.3 A 0.659339
AFFX-LysX-3_at 9.1 A 0.175328
AFFX-PheX-5_at 1.7 A 0.712257
AFFX-PheX-M_at 3.4 A 0.559354
AFFX-PheX-3_at 2.9 A 0.804734
AFFX-ThrX-5_at 1.1 A 0.932322
AFFX-ThrX-M_at 1.3 A 0.340661

Total number of rows: 57381

Table truncated, full table size 1932 Kbytes.

Supplementary file Size Download File type/resource
GSM262013.CEL.gz 8.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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