Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 12
Release date: Oct 3 2017
Last update date: Oct 11 2018
Access: Public
Chemicals: Pseudouridine
Dataset link A radiolabeling-free, qPCR-based method for locus-specific pseudouridine detection

Experimental Protocol


Here we report a radiolabeling-free, qPCR based method to rapidly detect Ψ in a locus-specific manner. The method is based on Ψ labelling adduct induced misincorporation during reverse transcription (RT), generating qPCR products of different melting temperatures. To demonstrate that read-through induced misincorporation is a general feature of Ψ sites under our improved RT condition, we utilized high-throughput sequencing to comprehensively examine the pattern of misincorporation for all Ψ sites in rRNA using HEK293T cells. Besides, to address the detection resolution of the method, three qPCR amplicons examined with our locus-specific approach were subjected to high-throughput sequencing (for MALAT1, EEF1A1 and 18S rRNA).

Repositories


GEO

GSE102476

ENA

SRP115188

BioProject

PRJNA397844

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Contact


Chengqi Yi