|
| Status |
Public on Mar 31, 2017 |
| Title |
Jun_19_2013_at_00:00_in_Toyama_DPS_54 |
| Sample type |
RNA |
| |
|
| Source name |
rice, leaf
|
| Organism |
Oryza sativa |
| Characteristics |
variety: Koshihikari
place: Toyama
sampling date: 6-19-13 0:00
days from transplanting to sampling: 54
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 2013/3/28, or 2013/4/18. The rice seedlings were transplanted on 2013/4/25, or 2013/5/15. The rice plants were grown in Toyama 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 |
02_13_0008
raw data file: S254663310018_A2.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) |
| GSE65604 |
Diurnal variation for rice leaves in Toyama field in 2013 |
|
