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Sample GSM1600843 Query DataSets for GSM1600843
Status Public on Mar 31, 2017
Title Aug_23_2013_at_20:00_in_Furukawa_DPS_71
Sample type RNA
 
Source name rice, leaf
Organism Oryza sativa
Characteristics variety: Koshihikari
place: Furukawa
sampling date: 8-23-13 20:00
days from transplanting to sampling: 71
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_0059
raw data file: S254663310066_A3.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 2.48171372991494
25 10.1385170925046
26 2.47769973447187
29 5.90625797528669
32 9.34270797579846
33 12.4184511348794
34 2.46560986436428
35 2.463825938552
36 11.310639299429
37 8.16397160699812
38 7.37059691531589
39 3.23159013637586
41 2.95805710656736
42 11.1029690096808
43 2.44861902634291
44 11.5010322892681
45 9.31039219453198
46 7.49074449943428
47 13.8278898401452
50 9.61203385475915

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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