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| Status |
Public on Apr 25, 2023 |
| Title |
5'RACE minus plant1 |
| 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 |
Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3' RACE-seq and 5' RACE-seq
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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_RACE_MINUS_5.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 3' end of the minus strand (Processed_data_RACE_MINUS_3.txt), for the 5 end of the minus strand (Processed_data_RACE_MINUS_5.txt) and for the 5 end of the plus strand (Processed_data_RACE_PLUS_5.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) or poly(U) tail sequence (polyX), poly(A) or poly(U) tail length (polyX.size), non-A or non U extension sequence (modification), length of the non-A or non-U extension (modification.size), tail sequence (extension), tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N or 8N 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) |
| GSE212355 |
Uridylation is a genomic feature of encapsidated GFLV RNAs [GFLV] |
| GSE212358 |
A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns |
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| Relations |
| BioSample |
SAMN30601271 |
| SRA |
SRX17360633 |
| 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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