|
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 |