Figure 3.

Identification and characterization of TEC-specific novel transcripts. (A) Validation of novel mT&T transcripts using ONT RNA sequencing. The fraction of novel transcripts supported by ONT reads are shown for mature mTEC (red) and immature mTEC (yellow). (B) Number of novel transcripts “uniquely” detected in mature mTEC and representative peripheral tissue samples (Supplemental Methods; Supplemental Figs. 3A, 8). (C) TEC-specific novel splicing events by event type and promiscuous expression status. Individual events may be counted in multiple categories. (SE) skipped exon; (RI) retained intron; (MX) mutually exclusive exon; (A3/A5) alternative 3′/5′ splice site; (AF/AL) alternative first/last exon. (D) Selected GO biological processes significantly overrepresented in the set of genes (n = 1167) from which the mTEC-specific novel transcripts were derived (one-sided Fisher's exact tests; BH adjusted P < 0.01). (E,F) Cdx1 and Mill1 are displayed as examples to show novel TEC-specific transcripts (red). Existence of the novel transcripts in mature mTEC was supported by both Illumina (Sashimi plots) and long-read ONT (selected reads) data. Novel transcripts are indicated by the “_N” suffix.