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| Status |
Public on Apr 25, 2023 |
| Title |
Purified virions GFLV K30 |
| Sample type |
SRA |
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| Source name |
Infected leaves of A. thaliana
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Infected leaves of A. thaliana
genotype: WT
treatment: GFLV
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| Growth protocol |
Leaves from GFLV infected plants
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| Extracted molecule |
total RNA |
| Extraction protocol |
Viral particles of GFLV K30 and B844 isolates were purified from C. quinoa by sucrose gradient. RNA was extracted from purified virions using phenol-chloroform.
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
Processed_Data_CAPSID_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: One processed data file is given. They includes the processed data for total RNA and RNA from purified virion of the K30 and B844 isolates. 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, Information about isolate et purification (Sample Description), 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
|
| Department |
IBMP
|
| 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 |
GPL17970 |
| Series (2) |
| GSE212356 |
Uridylation is a genomic feature of encapsidated GFLV RNAs [Purified virions] |
| GSE212358 |
A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns |
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| Relations |
| BioSample |
SAMN30601285 |
| SRA |
SRX17360621 |
| 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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