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Sample GSM436403 Query DataSets for GSM436403
Status Public on Aug 06, 2009
Title V. riparia (VR, PI588259) LD, 15h 28 days - rep1
Sample type other
 
Source name second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 28 days)
Organism Vitis riparia
Characteristics germplasm name: Vitis riparia pi588259
organism part: ud: 0000001 second order axillary bud
cell type: UD:0000001 second order axillary bud
development stage: UD:0000002 paradormancy
age: 58 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 with 15h day using supplemental 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 8695 P 0.000218932
1606427_at 364.37 P 0.000467603
1606428_at 29.526 P 0.00222774
1606429_at 17.843 P 0.0218664
1606430_at 1439.8 P 0.000218932
1606431_at 853 P 0.000218932
1606432_at 381.55 P 0.000218932
1606433_at 514.43 P 0.000804664
1606434_at 768.41 P 0.000218932
1606435_at 672.94 P 0.00358492
1606436_s_at 8283.4 P 0.000218932
1606437_at 915.65 P 0.000265668
1606438_at 574.02 P 0.000265668
1606439_s_at 3299.1 P 0.000218932
1606440_at 18.731 M 0.0439678
1606441_at 8.1901 A 0.458816
1606442_at 1805.4 P 0.000218932
1606443_at 18.75 A 0.127645
1606444_at 338.06 P 0.000265668
1606445_a_at 762.25 P 0.000218932

Total number of rows: 16602

Table truncated, full table size 505 Kbytes.




Supplementary file Size Download File type/resource
GSM436403.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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