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 profiling of rice embryogenic calli after Agrobacterium infection (Part 2-probe selection)
Weiwei Tie, Huazhong Agricultural University, College of Life Science and Technology, Wuhan, China (tieweiwei@webmail.hzau.edu.cn,weiweitie2011@gmail.com)
Experiment design (6 hybridizations)
genomic DNA
•Nipponbare gDNA •Zhensan gDNA

This experiment has been imported by PLEXdb from NCBI GEO (GSE32426)

Series_summary:
Agrobacterium tumefaciens-mediated genetic trans...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: Gene expression profiling of rice embryogenic calli after Agrobacterium infection (Part 2-probe selection)
Accession No: OS88
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
genomic DNA
•Nipponbare gDNA   •Zhensan gDNA
Quality Control: biological replicates
Treatment summary:
 genomic DNA  # replicates
 Nipponbare gDNA  3
 Zhensan gDNA  3
Total hybridizations: 6
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE32426)

Series_summary:
Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process.
In order to investigate the related genes affecting the transformation efficiency of embryogenic calli of different rice cultivars, we used Affymetrix GeneChip® Rice Genome Array to measure the global gene expression profiling just before transformation and at four different time points after transformation (1 h, 6 h, 12 h, 24 h) in both japonica rice cultivar Nipponbare and indica rice cultivar Zhenshan 97.

Series_overall_design:
The mature embryo-derived embryogenic calli of Nipponbare (Nip) and Zhenshan 97 (ZS) were infected by Agrobacterium. Calli of Nip and ZS were sampled just before infection (0 h) and 1h, 6h, 12 h and 24h after infection, respectively. Three independent biological replications for each time point of the two varieties were used. To avoid the influence of polymorphisms between the probe sequence on the array and the genomes of the varieties used, we used a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of gDNA from Nip and ZS with the PM oligonucleotide probes on the rice array. The genomic DNA of Nip and ZS were extracted and hybridized to the Affymetrix Rice Genome Arrays. Three biological replications per cultivar were performed.

PLEXdb Curator's Note:
At PLEXdb we have split the original expt. into two parts, one dealing with gene expression and the other probe-selection. This was necessary to build the experimental factors properly.

A. OS87 (Gene expression profiling of rice embryogenic calli after Agrobacterium infection- part1, gene expression): The main experiment dealing with gene expression in the two cultivars after Agrobacterium infection.

B. OS88 (Gene expression profiling of rice embryogenic calli after Agrobacterium infection- part2, probe-selection): Used for gDNA-based probe-selection strategy (''...genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of gDNA from Nip and ZS with the PM oligonucleotide probes on the rice array...'').
Publication: none
Created: 2012-04-03 11:56:39
Last Update: 2012-04-24 14:11:33
Released: 2012-04-26
GEO Accession GSE32426
Submitter: PLEXdb Curator
Name: Weiwei Tie
Institution: Huazhong Agricultural University, College of Life Science and Technology, Wuhan, China
Head of Laboratory: Yongjun Lin
email(s):
Homepage:

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

For problems with the webpages contact PLEXdb webmasters