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Sample GSM287900 Query DataSets for GSM287900
Status Public on Jul 15, 2008
Title Red soft berry C15 from plant 1 cluster distal position, biological rep 1
Sample type RNA
Source name grape berry near maturation
Organism Vitis vinifera
Characteristics Cultivar: Cabernet sauvignon
Treatment protocol Seleted grape berries were snap frozen upon harvest, prior to RNA extraction.
Growth protocol Dormant shoot cuttings of V. vinifera cv. Cabernet Sauvignon clone 15 were collected from a commercial vineyard near Osoyoos, BC, in January, 2006, and then transported on wet ice and stored at 4ºC.For fruit cluster propagation, a technique similar to that reported by Mullins and Rajasekaran (1981) was employed, as follows. The basipetal ends of several cuttings were scored with a razor blade and then placed in heated soil within a 4ºC walk-in cooler to promote root formation but inhibit bud break. After adventitious roots became visible, cuttings were moved to the greenhouse and potted in a mixture of 75% peat and 25% perlite (pH 7.0). On average, after nine days at 20-25ºC under a 16 h photoperiod, bud break occurred and a single cluster formed on the resulting shoot. Two shoots bearing healthy clusters were selected for experimentation.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated as described in Reid et al. 2006 (PMID: 17105665). One RNA extraction was done for each of 32 berries.
Label biotin
Label protocol Biotin -labeled cRNA was prepared according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).
Hybridization protocol Following fragmentation, 14 µg of cRNA from one berry was hybridized for 16 hr at 45ºC on each GeneChip Vitis (Grape) Genome Arrays . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned with an Affymetrix GeneArray 3000 7G scanner.
Description One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS)
Data processing The raw data were background adjusted, normalized and log2-transformed using the Bioconductor GCRMA package.
Submission date May 09, 2008
Last update date Jul 15, 2008
Contact name Steven T. Lund
Phone 604-822-5708
Fax 604-822-5143
Organization name The University of British Columbia
Department Wine Research Centre
Street address 241 - 2205 East Mall
City Vancouver
State/province BC
ZIP/Postal code V6T 1Z4
Country Canada
Platform ID GPL1320
Series (1)
GSE11406 Expression data in individual grape berries during ripening initation

Data table header descriptions
VALUE normalized signal

Data table
1606368_s_at 13.78411045
1606427_at 8.213283327
1606428_at 3.148703006
1606429_at 2.300044792
1606430_at 9.400857913
1606431_at 9.696215067
1606432_at 8.49390438
1606433_at 7.935857686
1606434_at 10.12569506
1606435_at 9.111081949
1606436_s_at 13.26708889
1606437_at 9.206337095
1606438_at 8.771343992
1606439_s_at 9.501473148
1606440_at 2.150099652
1606441_at 2.554869405
1606442_at 11.47977844
1606443_at 3.520287558
1606444_at 5.559525231
1606445_a_at 8.629465559

Total number of rows: 16602

Table truncated, full table size 376 Kbytes.

Supplementary file Size Download File type/resource
GSM287900_C15.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM287900_C15.CHP.gz 92.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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