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| Status |
Public on Apr 25, 2023 |
| Title |
TCV_urt1_1_Plant2 |
| Sample type |
SRA |
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| Source name |
Infected leaves
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Infected leaves
genotype: urt1-1
treatment: TCV
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| Growth protocol |
Leaves from GFLV, TuMV and TCV infected Arabidpsis plants (genotype WT, urt1-1, heso1-3 and heso1-3 urt1-1)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3'RACEseq
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_TCV_A.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: Three processed data files are given. They includes the processed data for the analyzed GFLV (Processed_data_GFLV_B1B2.txt), TuMV (Processed_data_TuMV_B1B2.txt) and TCV (Processed_data_TCV_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 |
GPL17970 |
| Series (2) |
| GSE212293 |
Involvement of Arabidopsis TUTases in viral RNA uridylation |
| GSE212358 |
A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns |
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| Relations |
| BioSample |
SAMN30600931 |
| SRA |
SRX17360535 |
| 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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