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Sample GSM6528532 Query DataSets for GSM6528532
Status Public on Apr 25, 2023
Title TBRV_RNA1&2_Plant1
Sample type SRA
 
Source name Infected leaves of V. vinifera
Organism Vitis vinifera
Characteristics tissue: Infected leaves of V. vinifera
genotype: WT
treatment: TBRV
Growth protocol Leaves from plants infected by Secoviruses
Extracted molecule total RNA
Extraction protocol Total RNA from infected leaves were extracted using the RNeasy plant Mini Kit (Qiagen).
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
Processed_Data_SECO_B2.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: A processed data file is given. It includes the processed data for the analyzed Secoviridae viruses for each 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, plant genotype (WT, urt1-1, heso1-3, heso1-3 urt1-1), 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 GPL29591
Series (2)
GSE212354 RNA uridylation percentages for virus of the Secoviridae family
GSE212358 A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns
Relations
BioSample SAMN30601093
SRA SRX17360559

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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