Kyle, Angela, Eric and Alex’s paper “Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)” is out in Methods! This is a very comprehensive manuscript, outlining the necessary background for understanding chemical probing of RNA structure – from the experiments that can generate the data all the way to the computational methods that can use the data to generate models of RNA structure (complete with command line instructions for running a suite of RNA structure prediction tools that can use SHAPE-Seq data). It also marks the official release of SHAPE-Seq 2.1, which combines the ‘universal’ RT priming strategy of SHAPE-Seq 2.0 with Kyle’s very clever PCR-based selection strategy from in-cell SHAPE-Seq to remove unwanted side reactions in library prep. This makes the dreaded side products all but disappear giving you more reads for your experiment!
We also added a few new experiments for both in vitro and in-cell probing of RNA structure, and as always all the data is freely available on RMDB. Finally, this publication comes at the same time of the official Spats v1.0 release for processing SHAPE-Seq datasets. Go team!