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:
Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems
Lauren M McIntyre, University of Florida, Department of Molecular Genetics and Microbiology (mcintyre@ufl.edu)
Experiment design (20 hybridizations)
Amplification method
•OneDirect •Pico
Nematode infection
•Control Root Cells •Giant Cells

This experiment has been imported by PLEXdb from NCBI GEO (GSE21981) Series_summary: Differential gene expression between groups of homogenous...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems
Accession No: AT99
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
Amplification method
•OneDirect   •Pico
Nematode infection
•Control Root Cells   •Giant Cells
Quality Control: biological replicates
Treatment summary:
 Amplification method  Nematode infection  # replicates
 OneDirect  Control Root Cells  5
 OneDirect  Giant Cells  5
 Pico  Control Root Cells  5
 Pico  Giant Cells  5
Total hybridizations: 20
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE21981)

Series_summary:
Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser capture microdissection. Arabidopsis root cells undergoing giant cell formation due to nematode infestation and un-infested control root cells were laser captured and used to evaluate 2 amplification systems. One, NuGEN's WT-Ovation Pico amplification system, uses total RNA as starting material while the other, NuGEN's WT-One-Direct Amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The NuGEN WT-Ovation One-Direct system was less reproducible and more variable than the NuGEN WT-Ovation Pico system. The NuGEN WT-Ovation Pico Amplification kit resulted in the detection of thousands of genes differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the NuGEN WT-Ovation One-Direct Amplification kit.

Series_overall_design:
Evaluation of each amplification system consisted of three biological replicates per treatment (control root cells or giant cells) with one biological replicate split into three technical replicates for a total of 10 samples per amplification procedure. RNA samples for amplification with the NuGEN WT-Ovation Pico kit were isolated from 150 control cells or from 80 giant cells using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). For amplification with the NuGEN WT-Ovation One-Direct kit, samples containing 150 control or 80 giant cells were collected directly into 2ul of the NuGEN lysis buffer. RNA amplifications were carried out according to the respective kits’ protocols.

PLEXdb Curator's Note:
The 5 replications are a combination of biological and technical reps. Each treatment consists of 3 biological replications and one of these three have 3 technical replications; making it a total of 5 reps. per treatment.

PLEXdb Curator's Note:

We want the users to be aware of the fact that some of the replications within a treatment have low correlation both after MAS5.0 and RMA normalization. One can see these plots by using the Treatmentrs Tab and then Show 'MAS/RMA Scatterplot'.

Publication: none
Created: 2010-09-27 13:48:02
Last Update: 2010-09-27 14:39:11
Released: 2010-10-19
GEO Accession GSE21981
Submitter: PLEXdb Curator
Name: Lauren M McIntyre
Institution: University of Florida, Department of Molecular Genetics and Microbiology
Head of Laboratory: Lauren M McIntyre
email(s):
Homepage:

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

For problems with the webpages contact PLEXdb webmasters