Fig. 2: isoCirc data of HEK293 cells.

a Heatmap showing pairwise comparison of similarity between high-confidence BSJs identified from six HEK293 libraries. Only BSJs with read count ≥2 were included. For each library pair, degree of similarity was calculated as number of shared high-confidence BSJs found in both libraries divided by total number of high-confidence BSJs in either library. Color reflects degree of similarity between two libraries, as indicated in legend. b Heatmap showing pairwise comparison of similarity between full-length circRNA isoforms (with read count ≥2) identified from six HEK293 libraries. Degree of similarity was determined as in (a). c Stacked barplot showing fraction of known or novel high-confidence BSJs identified in only one (‘1’) or both (‘2’) biological replicates of HEK293 cells, based on BSJ annotations in circBase (http://www.circbase.org) and MiOncoCirc (https://mioncocirc.github.io) databases. Only BSJs with read count ≥2 in each biological replicate (summing over three technical replicates) were included. Bars show known BSJs annotated in circBase only (red), MiOncoCirc only (blue), or both databases (‘Both’, green), and novel BSJs not annotated in either database (‘Novel’, purple). d Heatmap showing numbers of full-length circRNA isoforms identified in HEK293 cells, based on BSJ (x-axis) and FSJ (y-axis) categories as classified relative to existing transcript annotations. Only full-length circRNA isoforms with read count ≥2 (summing over all six libraries) were included. All identified circRNA BSJs and FSJs were classified using three categories: Full Splice Match (FSM), Novel In Catalog (NIC), and Novel Not in Catalog (NNC). e Long-read alignments (top) and gene structure diagrams (bottom) for the four most abundant full-length circRNA isoforms of KDM1A in HEK293 cells, as measured by isoCirc read count. All four isoforms were categorized as FSM for both BSJ and FSJs. Long-read alignments indicate multiple copies of circRNA templates in isoCirc reads. Inner black circle: circRNA gene structure with BSJ (red line) and FSJs (white lines). Blue circles: matched bases of isoCirc sequences aligned to reference genome sequence. Colored lines: mismatched bases (purple: A, red: C, green: G, yellow: T), insertions (black), and deletions (white), compared to reference genome sequence.