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| Status |
Public on Apr 25, 2023 |
| Title |
PVX biol rep2 |
| Sample type |
SRA |
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| Source name |
Infected leaves of N. benthamiana
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| Organism |
Nicotiana benthamiana |
| Characteristics |
tissue: Infected leaves of N. benthamiana
genotype: WT
treatment: PVX
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| Growth protocol |
Leaves from virus infected plants
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
RACE |
| Instrument model |
Illumina MiSeq |
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| Description |
3' RACE-seq
Processeddata_polyA_allvirus_B1B2.txt
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| 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).
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| Submission date |
Aug 30, 2022 |
| Last update date |
Apr 25, 2023 |
| Contact name |
Dominique Gagliardi |
| E-mail(s) |
dominique.gagliardi@ibmp-cnrs.unistra.fr
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| Organization name |
CNRS
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| Department |
IBMP
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| Street address |
12, rue du General Zimmer
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| City |
Strasbourg |
| ZIP/Postal code |
67084 |
| Country |
France |
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| Platform ID |
GPL22072 |
| 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 |
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| Relations |
| BioSample |
SAMN30601010 |
| SRA |
SRX17360602 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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