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Gene expression changes in Arabidopsis thaliana treated with Myzus persicae saliva
Dr. Martin De Vos, -- (gj32@cornell.edu)
Experiment design (6 hybridizations)
treatment
•Control •M-persicae saliva

This experiment has been imported by PLEXdb from NCBI GEO (GSE18960) Series_summary: Reference: De Vos and Jander, 2009 - Plant, Cell, and Env...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Gene expression changes in Arabidopsis thaliana treated with Myzus persicae saliva
Accession No: AT90
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
treatment
•Control   •M-persicae saliva
Quality Control: biological replicates
Treatment summary:
 treatment  # replicates
 Control  3
 M-persicae saliva  3
Total hybridizations: 6
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE18960)

Series_summary:
Reference: De Vos and Jander, 2009 - Plant, Cell, and Environment

Aim: Identification of genes responding to aphid saliva.

Background: During feeding on phloem sap aphids repeatedly salivate into the sieve element. It is thought that compounds in aphid saliva play a role in sustainable feeding. These compounds may include proteins and small molecules, which can function as virulence factors.

Growth conditions
Plants: Seeds of wild-type Arabidopsis thaliana (Col-0) were obtained from the were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix with Osmocoat fertilizer. Plants were grown in Conviron growth chambers in 20- x 40-cm nursery flats at a photosynthetic photon flux density of 200 mmol m-2 s-1 and a 16-h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. Plants were grown for 3 weeks and used in experiments before flowering. Aphids: All experiments were conducted with a tobacco-adapted red lineage of M. persicae. Aphids were raised on cabbage (Brassica oleracea) with a 16-h day (150 mmol m-2 s-1 at 24°C) and an 8-h night (19°C) at 50% relative humidity.

Experimental set-up/treatment:
Fifty aphids were allowed to feed from 50 µL artificial diet, containing sucrose and amino acids (Kim and Jander, 2007) between two layers of Parafilm. After 24 h, artificial diet from 20 aphids and control (0 aphids) diet cups was collected and infiltrated into leaves of intact Arabidopsis plants using a 1-mL syringe without the needle. Plants for control diet and aphid saliva containing diet were grown in the same pot to allow for a paired comparison. Eighteen leaves (3 leaves from 6 plants) treated with control and aphid saliva containing diet were harvested and immediately frozen in liquid nitrogen. This experiment was repeated 3 times to function as independent biological replicates.

RNA extraction + processing:
RNA was extracted using the Qiagen Plant RNeasy kit. RNA quality and quantity was assessed with an Agilent BioAnalyser 2100. Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips.

Data analysis:
Raw data from the microarrays was normalized at probe-level using gcRMA algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system. Significance of gene expression was determined using the LIMMA (Smyth, 2004) program and raw p values of multiple tests were corrected using False Discovery Rate (FDR).

Series_overall_design:
6 samples were used in this experiment
Publication: none
Created: 2010-09-14 13:46:17
Last Update: 2010-09-15 13:45:10
Released: 2010-09-24
GEO Accession GSE18960
Submitter: PLEXdb Curator
Name: Dr. Martin De Vos
Institution: --
Head of Laboratory: Dr. Georg Jander
email(s):
Homepage:

 
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