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Sample GSM6523464 Query DataSets for GSM6523464
Status Public on Apr 25, 2023
Title GRGV biol rep 3, TuMV biol rep 2
Sample type SRA
 
Source name Infected leaves of V. vinifera, or A. thaliana
Organisms Arabidopsis thaliana; Vitis vinifera
Characteristics tissue: Infected leaves of V. vinifera, or A. thaliana
genotype: WT
treatment: GRGV, TuMV
Growth protocol Leaves from virus infected plants
Extracted molecule total RNA
Extraction protocol Total RNA from infected leaves of C. quinoa, N. benthamiana and grapevine were extracted using the RNeasy plant Mini Kit (Qiagen). Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3' RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection RACE
Instrument model Illumina MiSeq
 
Description 3' RACE-seq
Processeddata_polyA_allvirus_B1B2.txt
Data processing Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: Two processed data file is given. They includes the processed data for the analyzed 21 virus, the poladenylated RNA virus (Processeddata_polyA_allvirus_B1B2.txt), and the non polyadenylated virus (Processeddata_nonpolyA_allvirus_A.txt) for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension), tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).
 
Submission date Aug 30, 2022
Last update date Apr 25, 2023
Contact name Dominique Gagliardi
E-mail(s) dominique.gagliardi@ibmp-cnrs.unistra.fr
Organization name CNRS
Department IBMP
Street address 12, rue du General Zimmer
City Strasbourg
ZIP/Postal code 67084
Country France
 
Platform ID GPL32612
Series (2)
GSE212292 Diversity of phytoviral RNA U-tailing among ss(+) RNA phytoviruses
GSE212358 A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns
Relations
BioSample SAMN30601003
SRA SRX17360609

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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