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 AraPLEX Experiment Data

Choose an experiment:
Genes affected by hog1 alleviation of CHS silencing
Nick Jordan, Department of Genetics, University of Cambridge
Experiment design (8 hybridizations)
genotype
•CHS-silenced type (ECG) •anthocyanin-producing revertants (15B)

This experiment submission is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database (http://ssbdjc2.nottingham.ac.uk/narrays/...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: Genes affected by hog1 alleviation of CHS silencing
Accession No: AT14
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•CHS-silenced type (ECG)  •anthocyanin-producing revertants (15B)
Quality Control: biological replicates
Treatment summary:
 genotype  # replicates
 CHS-silenced type (ECG)  4
 anthocyanin-producing revertants (15B)  4
Total hybridizations: 8
Description: This experiment submission is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database (http://ssbdjc2.nottingham.ac.uk/narrays/experimentbrowse.pl).The data was generated from NASC's Affymetrix service and offered for public access at BarleyBase.

If you publish with this data, please reference data from NASC/GARNet:

Craigon DJ., James N., Okyere J., Higgins J., Jotham J., May S.
NASCArrays: A repository for Microarray Data generated by NASC's Transcriptomics Service.
Nucleic Acids Research, (2004). volume 32, Database issue D575-D577.

Following is the original experiment description:

About the Experimenter
Name: Dr Nick Jordan
Head of Lab Name: Dr Ian Furner
Address: University of Cambridge
Department of Genetics
Downing Street
Cambridge

Postcode: CB2 3EH
Country: UK
Telephone Number: 01223 333959
Fax Number: 01223 333992

Experiment: Genes affected by hog1 alleviation of CHS silencing

Submitted to this database: 27/10/2003

Experiment Description

As part of an investigation into mechanisms of HDG silencing in Arabidopsis, we have produced transgenic plants containing extra copies of the chalcone synthase (CHS) gene. The CHS gene mediates an early step in the biosynthesis of the purple pigment anthocyanin. The insertion of extra copies of CHS in Arabidopsis caused the gene to be silenced in some plants. Seeds harvested from these CHS-silenced plants were mutated by treatment with ems. The progeny of these seeds were screened for "revertants" in which the effects of CHS silencing was alleviated and plants were able to produce anthocyanin. These revertants were found to contain a single recessive mutation; the trait has been termed hog1 (for homology dependant gene silencing 1). Our previous experiment used the Affymetrix 8200 chip to make comparisons between gene expression in the two genetic variants: the CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B). Results showed that there were over 100 genes with at least a 10-fold increase or decrease in expression. However, the variation between 2 reps of each genetic variant was high. We would now like to carry out a modified version of this experiment using the 25K Affymetrix chip. It is intended to increase the number of reps to 4, and take samples at an earlier stage than previously in order to decrease the effect of developmental spread. To reduce the effects of interplant variability, samples will be generated from total plant tissue from a pool of 10 plants at GS 1.04. RNA will be purified using RNeasy kits from Qiagen.
All of the data available in this website/database is free, and you are free to do whatever you please with it. If you intend to publish work based on any of this data, please acknowledge us, contact the experimenter above, and either acknowledge them or use them as co-authors in the work.

About this Experiment
Experiment Type: mutant/wildtype
Experimental Parameters: parameter mutant/wildtype
Quality Control Measures Taken: no-plants-pooled 10, biological-replicates 4
Publication: none
Created: 2004-06-10 09:34:41
Last Update: 2008-08-05 10:58:52
Submitter: Lishuang Shen
Name: Nick Jordan
Institution: Department of Genetics, University of Cambridge
Head of Laboratory: Dr Ian Furner
email(s):
Homepage:

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

For problems with the webpages contact PLEXdb webmasters