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TEV-Arabidopsis pathosystem

ABSTRACT: Transcription profiling of Arabidopsis plants infected with the Tobacco etch potyvirus TEV and the evolved TEV-At17, which was generated by serial passes of ancestral TEV in Arabidopsis. Infection with TEV-At17 cause severe symptoms in the plant, compared with the asymptomatic TEV-infection. Keywords: Virus infection

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE11088 | GEO | 2008/06/23

SECONDARY ACCESSION(S): PRJNA106961

REPOSITORIES: GEO

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TEV-Arabidopsis pathosystem

Project description:Transcription profiling of Arabidopsis plants infected with the Tobacco etch potyvirus TEV and the evolved TEV-At17, which was generated by serial passes of ancestral TEV in Arabidopsis. Infection with TEV-At17 cause severe symptoms in the plant, compared with the asymptomatic TEV-infection. Keywords: Virus infection Five replicates for each sample category (Arabidopsis Ler infected with mock, or with TEV and TEV-At17 viruses) were generated, and compared with a global reference, generated from an equimolar mix of amplified RNAs from each of the 15 plants. Three replicas (#1,2, and 3) in each group were labeled with Cy5 and compared with Cy3-labeled reference mix, while the other two replicas (#4 and 5) were reversed-labeled.

2008-06-23 | E-GEOD-11088 | biostudies-arrayexpress

potyvirus-Transcriptional analysis of Arabidopsis thaliana infected by a potyvirus.

Project description:ra03-02_potyvirus - potyvirus - Identification of genes involved in plant/virus interactions. - In this experiment, Arabidopsis plants infected by a virus, Tobacco etch virus (TEV), a potyvirus, were compared with healthy plants to identify genes for which the expression is modified by the viral infection. Analysis of both inoculated leaves and upper young leaves were performed 7 days after the inoculation with the virus (or with only buffer for the healthy plants). Keywords: normal vs disease comparison

2007-08-31 | GSE8875 | GEO

Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection

2012-07-04 | GSE37269 | GEO

Transcription profiling of Arabidopsis infected with Tobacco etch virus (TEV), a potyvirus vs healthy plants

Project description:In this experiment, Arabidopsis plants infected by a virus, Tobacco etch virus (TEV), a potyvirus, were compared with healthy plants to identify genes for which the expression is modified by the viral infection. Analysis of both inoculated leaves and upper young leaves were performed 7 days after the inoculation with the virus (or with only buffer for the healthy plants).

2005-11-01 | E-MEXP-364 | biostudies-arrayexpress

The transcriptomics of an evolved plant-virus gene-for-gene interaction

Project description: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.

2016-04-18 | GSE66020 | GEO

Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection

Project description:We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus. Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome This microarray can be useful to study gene activity of Arabidopsis thaliana associated with response to virus infection. For ecotypes ST-0, Wt-1, Ler-0, Di-2 there are five biological replicates and for ecotype Oy-0 there are three. As control we used four technical replicates of each ecotype, but five for Ler-0. Rows and columns are numbered as scanned by a GenePix Scanner (barcode on the bottom, DNA on the front surface).

2012-07-03 | E-GEOD-37269 | biostudies-arrayexpress

Viral fitness correlates with the magnitude and direction of the perturbation induced in the host's transcriptome: the tobacco etch potyvirus - tobacco case study.

Project description:Determination of fitness for viral genotypes is a standard practice in virology an essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype respect to a reference one, is a macroscopic property that captures into a single figure differences in performance at every stage of viral infection. To which extent the expression of certain host genes determines viral fitness? Can we identify host’s genes whose expression have a significant effect on viral fitness? To which functional classes and regulatory networks do belong these genes? We compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus (TEV) that differ in fitness. The larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Some genes were significantly altered by all genotypes while others depend on viral fitness. We identified genes whose expression showed a positive correlation with TEV fitness and genes with a negative one. To validate these correlations, we analyzed the expression of four positively and five negatively correlated genes. Over-expression of the first group activates hormone-mediated plant defense pathways. Under-expression of the second group reduces metabolism, growth and development and/or plant viral resistance, resulting in higher susceptibility

2018-03-05 | GSE99838 | GEO

Arabidopsis thaliana

Project description:Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection

| PRJNA159163 | ENA

Proteins associated wth Trypanosoma brucei HNRNPF/H

Project description:We aimed to find proteins associated with HNRNPH in bloodstream-form _Trypanosoma brucei_. We integrated a sequence encoding a cleavable TAP (Tandem Affinity Purification) tag into the genome upstream of, and in frame with, one _HNRNPH_ gene. The other allele was deleted. TAP-HNRNPH was purifed from triplicate lysates as shown under "Sample processing protocol". Sample processing protocol (30-5000chracters) The TAP-HNRNPH was bound to IgG beads, then released with Tobacco Etch Virus (TEV) protease. TAP-CFP served as the negative control. The His-tagged TEV protease was then removed using Ni-NTA-magnetic beads. Eluted proteins were separated on a 1.5 mm NuPAGE™ Novex™ 4-12 % Bis-Tris protein gel. For details see doi: 10.1371/journal.pone.0258903

2022-10-15 | PXD037289 | Pride

RBP40_arrays

Project description:In this study, we systematically identified the RNAs associated with a selective sample of 40 of ~600 yeast RNA-binding proteins (RBPs). To identify RNAs associated with each putative RBP, C-terminal tandem affinity purification (TAP)-tagged proteins, expressed under control of their native promoters, were affinity purified from whole cell extracts of cultures grown to mid-log phase in rich medium [1-3]. Extracts were incubated with immunoglobulin G (IgG) agarose beads, washed, and ribonuclear protein complexes were eluted by tobacco etch virus (TEV) protease treatment (Text S2). We performed two to four independent isolations with each tagged strain. As controls, we performed 13 immunoaffinity purifications (IPs) of untagged strains to identify and exclude potential false-positive RNA targets. We purified total RNA from the whole-cell extracts and TEV-purified fractions, reverse transcribed with an amino-allyl-dUTP/dNTP mix, coupled the purified cDNA to Cy3 and Cy5 dyes, respectively, mixed the two differentially labeled cDNA pools, and then hybridized them to DNA microarrays (Datasets S1-S4). An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Genotype: strain expressing tagged version of RNA-BP Keywords: all_pairs Computed

2010-06-25 | E-GEOD-13135 | biostudies-arrayexpress

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