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Sample GSM262016 Query DataSets for GSM262016
Status Public on Sep 22, 2008
Title Nipponbare, 4 days after infection with S. hermonthica, biological replicate #1
Sample type RNA
Source name Oryza sativa roots infected with Striga hermonthica at 4 days post-inoculation
Organism Oryza sativa Japonica Group
Characteristics synonym: Oryza sativa subsp. japonica
cultivar: Nipponbare
Age: 25 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 4 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 15.9 A 0.227636
AFFX-BioB-M_at 161.6 P 0.000052
AFFX-BioB-3_at 131.3 P 0.000044
AFFX-BioC-5_at 443.6 P 0.000044
AFFX-BioC-3_at 357.7 P 0.000052
AFFX-BioDn-5_at 555 P 0.000044
AFFX-BioDn-3_at 2081 P 0.000052
AFFX-CreX-5_at 4839.6 P 0.000044
AFFX-CreX-3_at 6477.4 P 0.000044
AFFX-DapX-5_at 4.8 A 0.354453
AFFX-DapX-M_at 5.4 A 0.52976
AFFX-DapX-3_at 2.9 A 0.852061
AFFX-LysX-5_at 1.3 A 0.631562
AFFX-LysX-M_at 4.7 A 0.5
AFFX-LysX-3_at 10.6 A 0.195266
AFFX-PheX-5_at 2 A 0.945787
AFFX-PheX-M_at 0.8 A 0.941572
AFFX-PheX-3_at 3.4 A 0.843268
AFFX-ThrX-5_at 2 A 0.824672
AFFX-ThrX-M_at 2.5 A 0.51489

Total number of rows: 57381

Table truncated, full table size 1934 Kbytes.

Supplementary file Size Download File type/resource
GSM262016.CEL.gz 8.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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