GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE88707 Query DataSets for GSE88707
Status Public on Sep 20, 2017
Title Parallel analysis of 5'-RNA ends in mock inoculated tomato plants
Organism Solanum lycopersicum
Experiment type Other
Summary 5′ RNA ligase mediated rapid amplification of cDNA ends (5′ RLM-RACE) is the widely used tool for confirming the direct cleavage of target mRNA by a miRNA. Recently, 5′ RLM-RACE combined with high-throughput sequencing such as parallel analysis of RNA ends (PARE) are gaining importance as these techniques allows to assess the large number of sample in a single experiment. In order to verify the cleavage of predicted a target mRNA in potato spindle tuber viroid (PSTVd) infected tomato plants, the the leaf samples collected from the mock inoculated (control/healthy) at 21-days were subjected for RNA extraction. A custom RNA adaptor containing MmeI restriction endonuclease was ligated to the free 5'-phosphate end of an uncapped mRNA using T4 RNA ligase, followed by reverse transcription (RT) and second strand synthesis using poly (T) primers. Obtained product was slightly amplified, cleaved with MmeI restriction endonuclease and then, a dsDNA adaptor was added to the 3’-end of the MmeI restriction endonuclease cleavage site. Resulted products were sequence in an Illumina Mi-Seq machine. Retrieved data was then used to verify the 5’-termini of predicted target mRNA.
Overall design In order to verify the PSTVd mediated cleavage of mRNAs, the PARE data obtained from control plants were compared with the PARE data obtained with PSTVd infected plants.
Contributor(s) Adkar-Purushothama CR, Perreault J
Citation(s) 28827569
Submission date Oct 13, 2016
Last update date May 15, 2019
Contact name Charith Raj Adkar-Purushothama
Organization name Université de Sherbrooke
Department Biochemistry
Street address 3201 rue Jean-Mignault
City Sherbrooke
State/province Quebec
ZIP/Postal code J1E 4K8
Country Canada
Platforms (1)
GPL20585 Illumina MiSeq (Solanum lycopersicum)
Samples (1)
GSM2344491 Tomato_Control (PARE)
BioProject PRJNA348319
SRA SRP091502

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
GSE88707_RAW.tar 20.0 Kb (http)(custom) TAR (of XLSX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap