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Sample GSM1565336 Query DataSets for GSM1565336
Status Public on Dec 16, 2014
Title 35L_3
Sample type RNA
 
Source name 15 berries incubated for 10 days under 35ºC/Light 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 4.3672314
13 6.6369925
14 4.7903876
15 3.6875114
16 5.6571655
17 11.034679
18 10.4728565
19 8.8287325
20 5.137817
21 4.092491
22 4.6820054
23 8.872076
24 4.432378
25 8.302137
26 10.722015
27 6.919819
28 8.0044365
29 8.400809
30 8.583114
31 4.6695375

Total number of rows: 43765

Table truncated, full table size 657 Kbytes.




Supplementary file Size Download File type/resource
GSM1565336_US22502608_252196310004_S01_GE1-v5_95_Feb07_1_3.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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