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Cell-Type Specific Features of Circular RNA Expression

Figure 1

Bioinformatic and statistical method for detecting circular isoforms.

A) We created a custom database of all UCSC known-gene annotated scrambled exon-exon junctions. By mapping paired end 76 nt sequencing reads from poly(A) depleted RNA, we detected thousands of distinct circular RNA isoforms, including many cases where multiple circular isoforms are transcribed from the same locus. Our informatic pipeline required that one read (read 1) map to a diagnostic exon x - exon y junction (y< = x) and the other read map within the inferred circular isoform. B) Statistical scores improve filtering: We modeled the distribution of alignment statistics for reads from under an empirical null. Estimating the empirical null distribution of alignment quality for read 1 (required to map to a diagnostic circular exon-exon junction) and read 2 (which need not be junctional) allows us to compute a per-circular isoform FDR and statistically identify artifacts. The bulk of detected circles (illustrated at right) have alignment profiles that distinguish them from those detected under the null model. We used an estimated FDR threshold of .025, shown on plot.

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1003777.g001