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Sample GSM1600822 Query DataSets for GSM1600822
Status Public on Mar 31, 2017
Title July_20_2013_at_06:00_in_Furukawa_DPS_36
Sample type RNA
 
Source name rice, leaf
Organism Oryza sativa
Characteristics variety: Koshihikari
place: Furukawa
sampling date: 7-20-13 6:00
days from transplanting to sampling: 36
tissue: leaf
Treatment protocol No particular treatment. The plants were grown according to practical cultivation at the sites.
Growth protocol The rice seeds were sown on 2013/4/18, or 2013/5/24. The rice seedlings were transplanted on 2013/5/24, or 2013/6/13. The rice plants were grown in Furukawa field.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Promega Maxwell 16 Instrument following manufacturer's instructions.
Label Cy5
Label protocol 200 ng of total RNA were reverse-transcribed and labelled using Low Input Quick Amp Labeling Kit following manufacturer's instructions. Labelled cRNA were purified with Qiagen RNeasy mini kit.
 
Hybridization protocol 825ng of labelled cRNA were hybridized using Gene Expression Hybridization Kit following manufacturer's instructions at NIAS RGRC Open Laboratory.
Scan protocol Scanned with Agilent G2505C.
Description 06_13_0012
raw data file: S254663310063_A4.txt
Data processing Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Signal after background detrend, multiplicative detrend and dye normalization by Agilent Feature Extraction Software and 'quantile' nomalization using normalize.qspline in affy package in R.
Data were filtered for cross-hybridization and probe design mistake (resulting ~125K data rows).
 
Submission date Feb 04, 2015
Last update date Mar 31, 2017
Contact name Takeshi Izawa
Organization name National Institute of Agrobiological Sciences
Street address 2-1-2 Kannondai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8602
Country Japan
 
Platform ID GPL19684
Series (1)
GSE65601 Diurnal variation for rice leaves in Furukawa field in 2013

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
23 2.94235845653048
25 9.49460102391092
26 3.04244165534602
29 6.40988025673995
32 7.26232036310221
33 11.7267177130597
34 2.90239337700042
35 6.37579936718954
36 12.2533074551596
37 6.91457374174007
38 7.69823676143205
39 5.88872561408744
41 3.2097949749918
42 10.1558162162288
43 2.85008919676845
44 11.369292676351
45 10.0334411628209
46 9.68997446201605
47 12.8600173553688
50 11.9998622732024

Total number of rows: 125722

Table truncated, full table size 2858 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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