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Sample GSM1565333 Query DataSets for GSM1565333
Status Public on Dec 16, 2014
Title 35D_2
Sample type RNA
 
Source name 15 berries incubated for 10 days under 35ºC/Dark condition
Organism Vitis labrusca x Vitis vinifera
Characteristics cultivar: Pione
tissue: grape berry just beginning to show color
Treatment protocol Grape berries just beginning to show color were collected from mature vines of 'Pione'; The berries were incubated for 10 days under one of four conditiond; 15ºC/Light, 15ºC/Dark, 35ºC/Light, 35ºC/Dark.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen samples by the hot borate method (Wan and Wilkins, 1994).
Label Cy3
Label protocol Total RNA (250 ng) was labelled with Cy3 according to the instructions for the Quick Amp Labeling Kit (Agilent, Palo Alto, CA). Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany).
 
Hybridization protocol Glass slides were hybridized overnight at 65 °C in a hybridization buffer containing a portion of Cy3 -labeled cRNA. After hybridization, slides were washed in Agilent Gene Expression Wash Buffer 1 (Agilent) with 0.005% Triton X-102 for 1 min at room temperature and Agilent Gene Expression Wash Buffer 2 (Agilent) with 0.005% Triton X-102 for 1 min at 37 °C.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565A) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Dec 15, 2014
Last update date Dec 16, 2014
Contact name Hiroshi Fujii
E-mail(s) hfujii@affrc.go.jp
Organization name Institute of Fruit Tree Science, NARO
Department Division of Citrus Research
Street address 485-6 Okitsunakacho, Shimizu
City Shizuoka
State/province Shizuoka
ZIP/Postal code 424-0292
Country Japan
 
Platform ID GPL19557
Series (1)
GSE64153 Microarray Analysis for the Screening of Genes Inducible by Light or Low Temperature in Post-veraison Grape Berries

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
12 3.6339161
13 6.4884214
14 3.3510752
15 4.670231
16 6.6074986
17 10.3337555
18 10.812494
19 7.982494
20 6.665285
21 4.928857
22 3.1443155
23 9.634996
24 4.3074417
25 9.8958845
26 9.553161
27 7.2764926
28 7.2755733
29 8.359565
30 8.260525
31 6.871686

Total number of rows: 43765

Table truncated, full table size 656 Kbytes.




Supplementary file Size Download File type/resource
GSM1565333_US22502608_252196310003_S01_GE1-v5_95_Feb07_1_4.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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