Search   for 
Find Your Gene ·  Publications ·  Tools ·  Gene List Suite ·  Expression Atlases ·  About PLEXdb ·  Feedback
Login ID:
Password:
Plants
Arabidopsis
Barley
Brachypodium
Citrus
Cotton
Grape
Maize
Medicago
Poplar
Rice
Soybean
Sugarcane
Tomato
Wheat
Pathogens & Symbionts
Search Experiments
Download Data
Gene List Suite
Tools
Your Account
Documentation
News
Personnel
Links
 Data Release Policy 
PLEXdb is committed to making expression data publicly available to researchers world-wide...
complete policy
 

Browse RicePLEX Experiment Data

Choose an experiment:
DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)
Zhi Liu, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China (liuzhi7667@hotmail.com)
Experiment design (60 hybridizations)
treatment
•HH1-30 •MH63-30 •HH1-60 •MH63-60 •HH1-75 •MH63-75 •HH1-90 •MH63-90 •HH1-HT •MH63-HT •HH1-LT •MH63-LT •HH1-Jxol •MH63-Jxol •HH1-Pxo99 •MH63-Pxo99 •HH1-Rs105 •MH63-Rs105 •HH1-Xv5 •MH63-Xv5

This experiment has been imported by PLEXdb from NCBI GEO (GSE33204)

Series_summary:
DNA microarray analysis has been proved to be an...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)
Accession No: OS75
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
treatment
•HH1-30   •MH63-30   •HH1-60   •MH63-60   •HH1-75   •MH63-75   •HH1-90   •MH63-90   •HH1-HT   •MH63-HT   •HH1-LT   •MH63-LT   •HH1-Jxol   •MH63-Jxol   •HH1-Pxo99   •MH63-Pxo99   •HH1-Rs105   •MH63-Rs105   •HH1-Xv5   •MH63-Xv5
Quality Control: biological replicates
Treatment summary:
 treatment  # replicates
 HH1-30  3
 MH63-30  3
 HH1-60  3
 MH63-60  3
 HH1-75  3
 MH63-75  3
 HH1-90  3
 MH63-90  3
 HH1-HT  3
 MH63-HT  3
 HH1-LT  3
 MH63-LT  3
 HH1-Jxol  3
 MH63-Jxol  3
 HH1-Pxo99  3
 MH63-Pxo99  3
 HH1-Rs105  3
 MH63-Rs105  3
 HH1-Xv5  3
 MH63-Xv5  3
Total hybridizations: 60
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE33204)

Series_summary:
DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. But the distribution of differentially expressed genes in GM crops remains unclear. So the results of microarray analysis might be invalid for assessment of unintended effects if differentially expressed genes are extremely distributed. We used microarrays to study the distribution pattern of differentially expressed genes in HH1 at different developmental stages and environmental conditions.

Series_overall_design:
Samples were collected from both HH1 and MH63 at different developmental stages and environmental conditions and were used for RNA extraction and hybridization on Affymetrix microarrays. We selected differentially expressed genes, common differentially expressed genes and common significantly changed pathways hoping to clarify the distributions of differentially expressed genes in HH1.

PLEXdb Curator's Note:
We were unable to determine a factorial structure for this design at GEO. The following list shows the factor names and the treatments as compiled from sample titles and descriptions from GEO sample pages.
---------------------------------
Factor Name :: Treatment (genotype, age, condition(temp/agent))
HH1-30 :: 30days , HH1 ,
MH63-30 :: 30days , wildtype ,
HH1-60 :: 60days , HH1 ,
MH63-60 :: 60days , wildtype ,
HH1-75 :: 75days , HH1 ,
MH63-75 :: 75days , wildtype ,
HH1-90 :: 90days , HH1 ,
MH63-90 :: 90days , wildtype ,
HH1-HT :: 30days , HH1 , High temp
M63-HT :: 30days , wildtype , High temp
HH1-LT :: 30days , HH1 , Low temp
MH63-LT :: 30days , wildtype , Low temp
HH1-Jxol :: 75days , HH1 , Jxol
MH63-Jxol :: 75days , wildtype , Jxol
HH1-Pxo99 :: 75days , HH1 , Pxo99
MH63-Pxo99 :: 75days , wildtype , Pxo99
HH1-Rs105 :: 75days , HH1 , Rs105
MH63-Rs105 :: 75days , wildtype , Rs105
HH1-Xv5 :: 75days , HH1 , Xv5
MH63-Xv5 :: 75days , wildtype , Xv5
---------------------------------
Publication: none
Created: 2011-12-01 09:43:18
Last Update: 2011-12-01 14:15:13
Released: 2011-12-01
GEO Accession GSE33204
Submitter: PLEXdb Curator
Name: Zhi Liu
Institution: Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
Head of Laboratory: Zhi Liu
email(s):
Homepage:

 
Copyright@2001-2013 The PLEXdb Group
All rights reserved.

For problems with the webpages contact PLEXdb webmasters