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Series GSE66020 Query DataSets for GSE66020
Status Public on Apr 18, 2016
Title The transcriptomics of an evolved plant-virus gene-for-gene interaction
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary We performed threefold evolution experiment with tobacco etch potyvirus isolate At17b (TEV-At17b) in five different ecotypes of Arabidopsis thaliana L. (Di-2, Ei-2, Ler-0, St-0, and Wt-1,), that are heterogeneous in their susceptibility to TEV-At17b infection. After the evolution phase, (i) we characterized the fitness and virulence of the evolved lineages across all host ecotypes, (ii) the molecular changes fixed in the viral genomes.
Next, we analyzed the transcriptoma of the plants using Agilent Microarray tecnology (i)plants infected with local adapted viral lineage, (ii)plants infected with evolved virus vs. ancestal virus, (iii) virus evolved in new host and infecting its original host, (iv) transcriptoma of most specialized and most generalized viruses infecting all five ecotypes.
 
Overall design We used at least 3 biological replicates for each sample category and as control we used mock inoculated plants. Plants of none sample category were mixed, but mantained as independent biological replicate. The data from ancestral viral strain TEV-At17b infecting A. thaliana ecotypes were taken at diferent time point (block 1) as data for evolved virus. Both sets of arrays were normalized on the whole.
 
Contributor(s) Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF
Citation(s) 27113435
Submission date Feb 18, 2015
Last update date Jul 18, 2016
Contact name Julia Hillung
E-mail(s) juhil1@ibmcp.upv.es
Organization name CSIC-UPV
Department IBMCP
Lab Hillung
Street address Ingeniero Fausto Elio s/n
City Valencia
State/province Valencia
ZIP/Postal code 46022
Country Spain
 
Platforms (1)
GPL12621 Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Probe Name version)
Samples (158)
GSM1612857 ecotype Ler-0_infected with lineage 1 of virus evolved in Ler-0_plant 2
GSM1612858 ecotype Ler-0_infected with lineage 1 of virus evolved in Ler-0_plant 3
GSM1612859 ecotype Ler-0_infected with lineage 1 of virus evolved in Ler-0_plant 4
Relations
BioProject PRJNA275700

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE66020_RAW.tar 1.4 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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