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Browse RicePLEX Experiment Data

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Expression data from rice seeds during low temperature treatment
Hong-Wei Xue, Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences, Shanghai, China (hwxue@sibs.ac.cn)
Experiment design (16 hybridizations)
cultivar
•Hanfeng •Zhonghua11
treatment
•4DAF-2d cold •4DAF-2d normal •4DAF •10DAF-2d cold •10 DAF-2d normal •10DAF

This experiment has been imported by PLEXdb from NCBI GEO (GSE31077)

Series_summary:
As a species mostly planted in tropical and subt...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression data from rice seeds during low temperature treatment
Accession No: OS90
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
cultivar
•Hanfeng   •Zhonghua11
treatment
•4DAF-2d cold   •4DAF-2d normal   •4DAF   •10DAF-2d cold   •10 DAF-2d normal   •10DAF
Quality Control: biological replicates
Treatment summary:
 cultivar  treatment  # replicates
 Hanfeng  4DAF-2d cold  2
 Hanfeng  4DAF-2d normal  0
 Hanfeng  4DAF  2
 Hanfeng  10DAF-2d cold  0
 Hanfeng  10 DAF-2d normal  0
 Hanfeng  10DAF  0
 Zhonghua11  4DAF-2d cold  2
 Zhonghua11  4DAF-2d normal  2
 Zhonghua11  4DAF  2
 Zhonghua11  10DAF-2d cold  2
 Zhonghua11  10 DAF-2d normal  2
 Zhonghua11  10DAF  2
Total hybridizations: 16
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE31077)

Series_summary:
As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized.
The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment.

Series_overall_design:
Whole plants of two rice cultivars Zhonghua11 (low temperature sensitive) and Hanfeng (low temperature tolerance) were treated at 14┬░C for 2 days during seed development stage. The plants without treatment serve as controls. Rice seeds were harvested for RNA extraction.


PLEXdb Curator's Note:
MAS and RMA box plots are not level, MAS quality control is below 85% correlation within treatment and RMA has a few below 90%.

Key to Sample Interpretation at PLEXdb:
DAF= days after fertilization
2DC = 2 days cold (2 days low temp treatment)

PLEXdb Sample Title GEO Sample Title
Hanfeng-4DAF-2D cold, biological rep1 Hanfeng_4D_2DC, biological rep1
Hanfeng-4DAF-2D cold, biological rep2 Hanfeng_4D_2DC, biological rep2
Hanfeng-4DAF-2D normal, biological 0 reps none
Hanfeng-4DAF, biological rep1 Hanfeng_4D, biological rep1
Hanfeng-4DAF, biological rep2 Hanfeng_4D, biological rep2
Hanfeng-10DAF-2D cold, biological 0 reps none
Hanfeng-10DAF-2D normal, 0 reps none
Hanfeng-10DAF- 0 reps none
Zhonghua11-4DAF-2D cold, biological rep1 Zhonghua_4D_2DC, biological rep1
Zhonghua11-4DAF-2D cold, biological rep2 Zhonghua_4D_2DC, biological rep2
Zhonghua11-4DAF-2D normal, biological rep1 Zhonghua_6D, biological rep1
Zhonghua11-4DAF-2D normal, biological rep2 Zhonghua_6D, biological rep2
Zhonghua11-4DAF, biological rep1 Zhonghua_4D, biological rep1
Zhonghua11-4DAF, biological rep2 Zhonghua_4D, biological rep2
Zhonghua11-10DAF-2D cold, biological rep1 Zhonghua_10D_2DC, biological rep1
Zhonghua11-10DAF-2D cold, biological rep2 Zhonghua_10D_2DC, biological rep2
Zhonghua11-10DAF-2D normal, biological rep1 Zhonghua_12D, biological rep1
Zhonghua11-10DAF-2D normal, biological rep2 Zhonghua_12D, biological rep1
Zhonghua11-10DAF, biological rep1 Zhonghua_10D, biological rep2
Zhonghua11-10DAF, biological rep2 Zhonghua_10D, biological rep2

Publication: none
Created: 2012-04-20 11:00:30
Last Update: 2012-04-24 14:44:37
Released: 2012-04-26
GEO Accession GSE31077
Submitter: PLEXdb Curator
Name: Hong-Wei Xue
Institution: Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences, Shanghai, China
Head of Laboratory: Hong-Wei Xue
email(s):
Homepage:

 
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