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Sample GSM298059 Query DataSets for GSM298059
Status Public on Oct 01, 2008
Title Crown tissue of Harnesk at 3 weeks post germination, biological rep 1
Sample type RNA
 
Source name Harnesk crown 3 weeks post-germination
Organism Triticum aestivum
Characteristics variety: Harnesk
Grown for three weeks with 14 hour photoperiod; 16°C day 14°C night; PAR = 280.
Growth protocol Seeds were planted in 50:50 potting compost:perlite in 10 cm pots and maintained in growth cabinets with a 14 h photoperiod (PAR 280) and 16°C day/14°C night. After three weeks of these conditions, plants were gradually exposed to a decline in temperature, day-length and light intensity: week 3-4 = 14 h photoperiod (PAR 280), 14°C day/12°C night; week 4-5 = 12 h photoperiod (PAR 185), 14°C day/10°C night;week 5--6 = 11 h photoperiod (PAR 185), 12°C day/10°C night;week 6-7 = 11 h photoperiod (PAR 185), 12°C day/8°C night;week 7-8 = 10 h photoperiod (PAR 95), 10°C day/6°C night;week 8-9 = 9 h photoperiod (PAR 95), 8°C day/4°C night;week 9-10 = 8 h photoperiod (PAR 95), 6°C day/2°C night;week 10-11 = 8 h photoperiod (PAR 95), 4°C day/2°C night;week 11-12 = 8 h photoperiod (PAR 48), 2°C day/2°C night.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChip Wheat Genome Arrays wee scanned with the GeneChip 3000.
Description Plants 3 weeks post-germination treated with standard conditions (14 hour photoperiod; 16°C day 14°C night; PAR = 280). These are the reference samples for the determination of change in gene expression.
Data processing The data were analysed using GeneSpring GX 7.3: raw data was imported from .CEL files and normalised using RMA. Within GeneSpring GX, per gene normalisation to the median was perfored.
 
Submission date Jun 12, 2008
Last update date Jul 02, 2008
Contact name Mark Owen Winfield
E-mail(s) Mark.Winfield@bristol.ac.uk
Phone 07753191981
Organization name Bristol University
Department Biological Sciences
Lab OB120
Street address Woodland Road
City Bristol
ZIP/Postal code BS8 1UG
Country United Kingdom
 
Platform ID GPL3802
Series (1)
GSE11774 Expression data from cold treated wheat cultivars

Data table header descriptions
ID_REF
VALUE GeneSpring GX normalised value.

Data table
ID_REF VALUE
AFFX-BioB-3_at 0.905
AFFX-BioB-5_at 0.946
AFFX-BioB-M_at 0.990
AFFX-BioC-3_at 0.834
AFFX-BioC-5_at 0.859
AFFX-BioDn-3_at 0.844
AFFX-BioDn-5_at 0.793
AFFX-CreX-3_at 0.905
AFFX-CreX-5_at 0.838
AFFX-DapX-3_at 0.746
AFFX-DapX-5_at 0.818
AFFX-DapX-M_at 0.743
AFFX-LysX-3_at 0.554
AFFX-LysX-5_at 0.844
AFFX-LysX-M_at 0.791
AFFX-PheX-3_at 0.791
AFFX-PheX-5_at 0.756
AFFX-PheX-M_at 0.871
AFFX-r2-Bs-dap-3_at 0.722
AFFX-r2-Bs-dap-5_at 0.871

Total number of rows: 61290

Table truncated, full table size 1509 Kbytes.




Supplementary file Size Download File type/resource
GSM298059.CEL.gz 5.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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