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Status |
Public on Oct 12, 2017 |
Title |
Computational guideline for small RNA profiling in virus-infected plants |
Organism |
Arabidopsis thaliana |
Experiment type |
Non-coding RNA profiling by high throughput sequencing
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Summary |
We describe a series of computational pipelines for the in silico analysis of small RNAs (sRNA) produced in response to viral infections in plants. Our workflow is primarily focused on the analysis of sRNA populations derived from known or previously undescribed viruses infecting host plants. Furthermore, we provide an additional pipeline to examine host-specific endogenous sRNAs activated or specifically expressed during viral infections in plants. We present some key points for a successful and cost-efficient processing of next generation sequencing sRNA libraries, from purification of high quality RNA to guidance for library preparation and sequencing strategies. We report a series of free available tools and programs as well as in-house Perl scripts to perform in-house sRNA-seq data mining. A multi-step analysis pipeline is extensively detailed so previous bioinformatic background is not required, but experience with basic Unix commands is desirable.
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Overall design |
sRNAseq from Arabidopsis leaves non-infected and infected with Tobacco rattle virus (TRV)
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Contributor(s) |
Donaire L, Llave C |
Citation missing |
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Submission date |
Oct 11, 2017 |
Last update date |
Jul 25, 2021 |
Contact name |
Livia Donaire |
E-mail(s) |
ldonaire@cebas.csic.es
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Phone |
0034968396200
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Organization name |
Centro de EdafologĂa y BiologĂa Aplicada del Segura
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Department |
Plant Pathology
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Street address |
Campus de Espinardo
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City |
Murcia |
State/province |
Murcia |
ZIP/Postal code |
30100 |
Country |
Spain |
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Platforms (1) |
GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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Samples (2) |
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Relations |
BioProject |
PRJNA413879 |
SRA |
SRP119725 |