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Status |
Public on May 18, 2011 |
Title |
stage 2 transplanted on June 13_20080812_11_st2_n1 |
Sample type |
RNA |
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|
Channel 1 |
Source name |
rice, leaf, Norin 8
|
Organism |
Oryza sativa |
Characteristics |
genotype: Norin 8 developmental stage: stage 2 transplanted on June 13 sampling time: Aug 12, 2008, at 11 am
|
Treatment protocol |
Rice leaves were sampled at the paddy field. Cut leaves were frozen using liquid N imeditately after sampling. 2h interval. From 7:00am on Aug.12th to 7:00 a.m. on Aug.13th.
|
Growth protocol |
Rice plants were grown in a paddy field in Tsukuba, Japan on 2008 using a typical cultivation method. Transplanting dates were June 6, June 13, June 20, June 27 to obtain RNA from plants at different developmental stages on the sampling date.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extracted using QIAGEN RNeasy Plant Mini Kit following manufacturer's instructions
|
Label |
Cy3
|
Label protocol |
400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using NTP and 400 µM Cy3 CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.
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Channel 2 |
Source name |
rice, leaf, osgi
|
Organism |
Oryza sativa |
Characteristics |
genotype: osgi developmental stage: stage 2 transplanted on June 13 sampling time: Aug 12, 2008, at 11 am
|
Treatment protocol |
Rice leaves were sampled at the paddy field. Cut leaves were frozen using liquid N imeditately after sampling. 2h interval. From 7:00am on Aug.12th to 7:00 a.m. on Aug.13th.
|
Growth protocol |
Rice plants were grown in a paddy field in Tsukuba, Japan on 2008 using a typical cultivation method. Transplanting dates were June 6, June 13, June 20, June 27 to obtain RNA from plants at different developmental stages on the sampling date.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extracted using QIAGEN RNeasy Plant Mini Kit following manufacturer's instructions
|
Label |
Cy5
|
Label protocol |
400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using NTP and 400 µM Cy5 CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.
|
|
|
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Hybridization protocol |
825ng of labeled cRNA were used for hybridization according to manufacturer's protocol. Open-lab in rgrc in NIAS was used.
|
Scan protocol |
Scanned on an Agilent G2505B scanner.
|
Description |
20080812_11_st2_n1
|
Data processing |
Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1). LOWESS normalization.
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Submission date |
Oct 22, 2009 |
Last update date |
May 20, 2011 |
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 |
GPL6864 |
Series (1) |
GSE18685 |
Time-course in rice leaves in the field: WT (cv.Norin8) vs. osgi mutant |
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