Fig. 2
Identification of HOTAIR isoforms in differentiating ASCs. a Bioinformatic pipeline for identification of HOTAIR isoforms. b Representative integrative genomics viewer (IGV) tracks for short-read Illumina RNA-seq (upper) and PacBio capture-seq (lower) coverage tracks on HOTAIR (D0). c Venn diagram showing the overlap between HOTAIR isoforms identified using TAMA and Cupcake ToFU. d-h SQANTI characterization of 34 HOTAIR transcripts, with: (d) Number of isoforms per SQANTI categories and presence of non-canonical splice sites. e Distance in base pairs from the isoform start to the nearest CAGE peak summit from Ref. [34]. f HOTAIR exon E7 diagram showing 3’ end polyA tails. g Cumulative read counts of the isoforms shown by SQANTI categories. h Cumulative read number per isoform vs. number of samples in which the isoform was detected (cutoff: 0.1 × 103 reads per isoform). i Exon structure of 23 high confidence HOTAIR isoforms colored by SQANTI categories. FSM: full splice match; ISM: incomplete splice match; NIC: novel in catalog; NNC: novel not in catalog