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Sample GSM2735616 Query DataSets for GSM2735616
Status Public on Dec 01, 2019
Title S Habrochaitis, FnyCMV
Sample type SRA
 
Source name shoot apex
Organism Solanum habrochaites
Characteristics infection status: infected with Cucumber mosaic virus
tissue: shoot apex
Treatment protocol the seedlings at 2-3 leaf stage were inoculated with viral RNA. The apical part of the plants were harvested at 9-10dpi.
Growth protocol the plants were grown in Conviron Chambers set at 28 and 22°C ( day and ngiht, respectively) with 16 hours of light
Extracted molecule total RNA
Extraction protocol total RNA was extracted using Tri-reagent and 1.5 ug of total RNA was used for small RNA library construction using Illumina sRNA construction kit version 1.5
Illumina compatible method using standard Illumina adapters
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Data processing the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v3.2
Supplementary_files_format_and_content: csv, raw abundances
 
Submission date Aug 08, 2017
Last update date Dec 01, 2019
Contact name Tamas Dalmay
E-mail(s) T.dalmay@uea.ac.uk
Phone +44 1603593221
Organization name University of East Anglia
Department School of Biological Sciences
Street address Earlham Road
City Norwich
ZIP/Postal code NR4 7TJ
Country United Kingdom
 
Platform ID GPL23877
Series (1)
GSE102373 Mechanisms of RNA virus induced plant death
Relations
BioSample SAMN07462244
SRA SRX3071588

Supplementary file Size Download File type/resource
GSM2735616_S8.csv.gz 28.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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