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Specifications


Application: RNA-seq analysis, sRNA-seq analysis
Number of samples: 29
Release date: Sep 16 2016
Last update date: Dec 16 2016
Access: Public
Diseases: Tumor Virus Infections
Chemicals: Nucleotides
Mutations: p|SUB|CYM|19|X
Dataset link Distinct effects of p19 RNA silencing suppressor on small RNA mediated pathways in plants

Experimental Protocol


In this study we analyzed how p19 of CymRSV interacts with small RNAs and how this effects AGO1 and AGO2 in Nicotiana benthamiana. To have a better understanding on how p19 works with or without viral background we used wild type and synthetic p19 expressing plants (p19syn) combined with wild type and p19 deficient CymRSV (cym19stop). We made small RNA seq from RNAs co-immunoprecipitating with p19 from samples where p19 was expressed trans (p19syn x cym19s ), expressed cis (wt Nb x CymRSV) and p19 without viral background (p19syn x mock inoculation). Input samples for each were also sequenced for comparing. mRNA seq were made from direct RNA extraction from a parallel experiments. AGO1 and AGO2 immunoprecipitation were made from mock, cym19s and CymRSV infected plants. Small RNAs from the input and pulldown samples were sequenced. A biological replicate was made to enhance reliability. Small RNA seq was made from RNA directly extracted from Cym19s A biological repeat was made to increase credibility of the small RNA sequencing of small RNAs co-immunoprecipitating with AGO1 and AGO2. This experiment was conducted exactly as the previous one.

Repositories


GEO

GSE77070

ENA

SRP068742

BioProject

PRJNA309389

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Contact


Várallyay Éva

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