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Sample GSM1601318 Query DataSets for GSM1601318
Status Public on Mar 31, 2017
Title Aug_22_2014_at_08:00_in_Sapporo_DPS_84
Sample type RNA
 
Source name rice, leaf
Organism Oryza sativa
Characteristics variety: Koshihikari
place: Sapporo
sampling date: 2014/08/22 08:00
days from transplanting to sampling: 84
tissue: leaf
Treatment protocol No particular treatment. The plants were grown according to practical cultivation at the sites.
Growth protocol The rice seedlings were transplanted on 2014/5/22, or 2014/5/30. The rice plants were grown in Sapporo field.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Promega Maxwell 16 Instrument following manufacturer's instructions.
Label Cy3
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 07_14_0140
raw data file: S254663310177_A1.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)
GSE65609 Diurnal variation for rice leaves in Sapporo field in 2014

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
23 2.19816108882305
25 10.0612761578964
26 2.19612483014791
29 6.60736559188995
32 8.94568304626275
33 11.9563104504071
34 2.18824153643405
35 2.1766973091278
36 12.6057696643374
37 7.59896195182987
38 8.06391430295477
39 3.8285181590827
41 2.18473052286887
42 10.8963548807493
43 2.1708375922939
44 11.5886686085746
45 9.97180164778091
46 8.70500578998518
47 13.3636237236179
50 10.9470527847976

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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