Additional file 6: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

FIRRE exon junctions confirmed by amplicon sequencing. All reads were mapped against hg19 without reference to transcript annotation: Amplicons using convergent primer pairs and divergent primer pairs (to amplify circRNAs only) are shown separately. Canonical junctions were mapped using MapSplice [67], circRNA (back-splice) junctions were mapped using PTESFinder [46]. For details, see methods. Exon number is according to schema in Fig. 6b. Junction position (hg19), amplicons of origin, and junction frequencies, are given for all junctions. Only splices with a frequency of 1% or higher in each amplicon, identified either by MapSplice or PTESfinder, are reported. Canonical junctions present within the current FIRRE annotation are show in blue. All others are not present within current annotation. Off target junctions (presumed to be generated by illegitimate primer binding) are also shown. Data is for confirmation of junction presence within transcripts only: Junction frequency is affected by position relative to primer, size dependent amplification bias during Nextera indexing, and size dependent bias in cluster formation/resolution efficiencies during MiSeq sequencing. (XLSX 71Â kb)