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Sample GSM436372 Query DataSets for GSM436372
Status Public on Aug 06, 2009
Title Seyval (SV, Seyve Villard 5-276) SD, 13h 3 days - rep3
Sample type other
 
Source name second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 3 days)
Organism Vitis hybrid cultivar
Characteristics germplasm name: seyval (seyve-villard 5-276)
organism part: ud: 0000001 second order axillary bud
cell type: UD:0000001 second order axillary bud
development stage: UD:0000003 endodormancy
age: 33 days after bud break
growth media: peat/perlite/soil
Growth protocol Growth Description: Three to four shoots were trained vertically on spur pruned greenhouse grown vines. Vines were watered two times daily at 8:30 am and 3:00 pm. Environmental Conditions: Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (3 days at 13h). Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.
Extracted molecule other
Extraction protocol Modified Pine Buffer RNA Extraction Procedure
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007; V. riparia on 3/26/2007) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). At 1, 3, 7, 14, 21, 28 and 42 days of additional LD or SD, buds were harvested from nodes 3 to 12 from shoot base, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date.
Data processing The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.
 
Submission date Aug 04, 2009
Last update date Aug 05, 2009
Contact name PLEXdb Curator, Sudhansu Dash
Organization name Iowa State University
Department Virtual Reality Application Center
Lab PLEXdb
Street address 1023 Crop Genomes Informatics Lab (Iowa State University)
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platform ID GPL1320
Series (1)
GSE17502 Photoperiod regulation of grape bud dormancy

Data table header descriptions
ID_REF Affymetrix probe set id
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1606368_s_at 11756 P 0.000218932
1606427_at 341.68 P 0.000265668
1606428_at 145.07 P 0.0149365
1606429_at 30.562 A 0.218983
1606430_at 1601.5 P 0.000218932
1606431_at 847.29 P 0.000218932
1606432_at 346.5 P 0.000218932
1606433_at 3280.1 P 0.000467603
1606434_at 765.01 P 0.000218932
1606435_at 251.47 P 0.00222774
1606436_s_at 10509 P 0.000218932
1606437_at 1516.9 P 0.000321571
1606438_at 871.35 P 0.000321571
1606439_s_at 4131.2 P 0.000218932
1606440_at 14.394 A 0.52062
1606441_at 30.299 A 0.066865
1606442_at 2280.7 P 0.000218932
1606443_at 5.8065 A 0.697453
1606444_at 679.3 P 0.00038826
1606445_a_at 777.81 P 0.000218932

Total number of rows: 16602

Table truncated, full table size 502 Kbytes.




Supplementary file Size Download File type/resource
GSM436372.CEL.gz 1.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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