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:
Gene expression of rice root tips before, at and buckled by a hard layer in two rice varieties
Gareth,,Norton, University of Aberdeen , Aberdeen , United Kingdom (g.norton@abdn.ac.uk)
Experiment design (12 hybridizations)
genotype
•Azucena •Bala
root response
•at wax level •buckled at wax level •before wax level

This experiment has been imported by PLEXdb from NCBI GEO (GSE10857)

Series_summary:
The aim of this study was to determine the chan...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: Gene expression of rice root tips before, at and buckled by a hard layer in two rice varieties
Accession No: OS20
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•Azucena   •Bala
root response
•at wax level   •buckled at wax level   •before wax level
Quality Control: biological replicates
Treatment summary:
 genotype  root response  # replicates
 Azucena  at wax level  3
 Azucena  buckled at wax level  3
 Azucena  before wax level  3
 Bala  at wax level  3
 Bala  buckled at wax level  0
 Bala  before wax level  0
Total hybridizations: 12
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE10857)

Series_summary:
The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer.
Two genotypes (Azucena and Bala) that vary in there ability to penetrate a hard layer were selected for a genotype comparison of gene expression at the hard layer.

Keywords: Genotype comparison, root impedance response

Series_overall_design:
A chamber with the internal dimensions of 10 x 5 x 25cm consisting of a glass back, Perspex front and aluminium spacers with an open bottom and top was set at an angle of 15o in a large sand filled tray and filled up to 19.5 cm with dry sand. The sand was watered with nutrient solution, the sand was levelled and then a 5mm thick 60% wax layer (prepared using a ratio of 3:2 (w/w) of pastillated paraffin wax / white soft wax) was poured on the sand. Once the wax layer had set, two small holes were placed at the back of the wax layer to allow water drainage and water exchange via capillary action. The chamber was then filled up with more dry sand, and then watered using nutrient solution. Nutrient solution was then added to the large tray which the chamber had been placed; this was regularly topped up and allowed the watering of the chamber by capillary action. Light was eliminated from the chambers using white (exterior face)/black (interior face) plastic sheeting.
Azucena and Bala seeds were surface sterilized with 1% (v/w) sodium hypochlorate for 5 minutes, then rinsed thoroughly three times with water and then germinated on moist tissue paper for 48 hours at 37oC. A single germinated seed was then sown 1 cm below the surface of the sand in each chamber.
The plants were grown in a controlled environment room with a 12 hour day and night, with a day temperature of 30oC and a night temperature of 24oC with 300 ┬Ámol m-2 s-1 PAR. After 24 days the chamber was dismantled and the root tips of 5 mm length were harvested from Azucena plants for subsequent RNA extractions from the three categories as follows; a) roots which were between 5-10 mm above the wax layer; b) roots at the wax layer; c) roots which had buckled at the wax layer and grown 7-10 mm after buckling. From Bala plants, only root tips at the layer were harvested.

Each condition was independently replicated 3 times.
Publication: none
Created: 2009-05-21 14:22:07
Last Update: 2009-05-21 14:39:16
GEO Accession GSE10857
Submitter: PLEXdb Curator
Name: Gareth,,Norton
Institution: University of Aberdeen , Aberdeen , United Kingdom
Head of Laboratory: --
email(s):
Homepage:

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

For problems with the webpages contact PLEXdb webmasters