Fig. 4

Full-length RNA-seq analysis of dysplastic HSCs. a Number of ISO-seq-identified transcripts overlapping with repeats. b Representation of multiexonic or monoexonic repeat-overlapping transcripts, according to the transcript structure in ISO-seq transcriptome. c–e Structure of representative ISO-seq-identified transcripts. Dark red indicates novel, previously unannotated transcripts identified by both ISO-seq and de novo transcript assembly. Previously annotated transcripts are indicated in green in the ISO-seq track and the corresponding GENCODE transcripts in black. De novo-assembled transcripts confirmed by ISO-seq or present in GENCODE v29 annotation are indicated in dark blue. Dotted red boxes indicate the retained introns. RNA-seq read coverage in representative samples is also illustrated as a separate track. f Expression of novel intron-retaining ISO-seq-identified and de novo-assembled transcripts (intron retained), in comparison with the respective index fully spliced transcript (intron spliced) in healthy and pre-treatment dysplastic HSCs. HSCs from all untreated patients from both cohorts are shown