Multiplexed Detection and Analysis of Low-Abundance Long Noncoding RNA Using RNAscope™ in Cultured Cells

Abstract

Detecting low-abundance long noncoding RNAs (lncRNAs) is extremely difficult due to their expression levels. Deeper sequencing with extensive protocols is required to detect these RNAs and high-throughput screens to examine the regulation of these RNAs are challenging. This protocol provides a multiplexed and robust method of detecting low-abundance RNAs, with improved signal-to-noise ratio using RNAscope-based RNA-FISH which utilizes a series of amplification steps. We have validated this protocol for investigating the regulation of low-abundance lncRNAs, which would be ideal for in vitro screening in 96-well plates.