Cotranscriptional SHAPE-seq of E. coli thiB riboswitch for all lengths with 0mM TPP, replicate 1
DNA templates were prepared consisting of a consituitive E. coli promoter followed by the E. coli thiB riboswitch sequence with randomly incorporated biotinylated dNTPs as described previously (doi: 10.1093/nar/gkx233).  DNA template library was incubated with streptavidin after creating open complexes with E.coli RNA polymerase, followed by initiating in vitro transcription by adding MgCl2 to the reaction. Reactions were then incubated at 37C for 30s before being probed with BzCN (+)  or DMSO (-), and then transcribed and probed RNA is extracted with Trizol.  Extracted RNAs were then processed according to the SHAPE-Seq v2.1 protocol for cDNA syntehsis and illumina library preparation prior to sequencing (doi:10.1016/j.ymeth.2016.04.002).