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Series GSE75768 Query DataSets for GSE75768
Status Public on Jun 15, 2019
Title Parallel analysis of 5'-RNA ends in PSTVd-M 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 validate the cleavage of predicted a target mRNA in potato spindle tuber viroid-mild (PSTVd-M) infected tomato plants, the leaf samples collected at 21-days post inoculation 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 Verification of RISC mediated cleavage of target mRNAs by PSTVd-M derived small RNA.
Contributor(s) Adkar-Purushothama CR, Perreault J
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Submission date Dec 07, 2015
Last update date Jun 17, 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)
GSM1967131 Tomato_PSTVd-M (PARE)
BioProject PRJNA305298
SRA SRP067081

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Supplementary file Size Download File type/resource
GSE75768_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

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