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Series GSE104799 Query DataSets for GSE104799
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
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.
 
Overall design sRNAseq from Arabidopsis leaves non-infected and infected with Tobacco rattle virus (TRV)
 
Contributor(s) Donaire L, Llave C
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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
Phone 0034968396200
Organization name Centro de EdafologĂ­a y BiologĂ­a Aplicada del Segura
Department Plant Pathology
Street address Campus de Espinardo
City Murcia
State/province Murcia
ZIP/Postal code 30100
Country Spain
 
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (2)
GSM2808011 MOCK8
GSM2808012 TRV8
Relations
BioProject PRJNA413879
SRA SRP119725

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104799_RAW.tar 2.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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