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Status |
Public on Apr 25, 2023 |
Title |
TuMV_WT_Plant1 |
Sample type |
SRA |
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Source name |
Infected leaves
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Organism |
Arabidopsis thaliana |
Characteristics |
tissue: Infected leaves genotype: WT treatment: TuMV
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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_TuMV_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: 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 |
SAMN30600959 |
SRA |
SRX17360507 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Processed data are available on Series record |
Raw data are available in SRA |
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