Fig. 1: Identification of a core subset of vascular lineage-specific lncRNAs.

a Schematic representation of the analysis pipeline. Total RNA was extracted from two replicates of neonatal lymphatic and blood vascular endothelial cells (LECs and BECs) derived from the same donor and subjected to both RNA-Seq and Cap Analysis of Gene Expression (CAGE-Seq). Neonatal dermal fibroblasts (DFs) data from FANTOM6 database³³ were included to increase endothelial cell specificity. After differential expression (DE) analysis using EdgeR³⁴, we overlapped the results from RNA-Seq and CAGE-Seq data to select lncRNAs differentially expressed in both techniques. b, c MA plots displaying log₂ fold change (log₂FC) against expression levels (logCPM) of DE genes after RNA-Seq b and CAGE-Seq c between LECs and BECs. Green and red dots: LEC- and BEC-specific lncRNAs (FDR < 0.01); light green and light red dots: lncRNAs excluded from the analysis because also expressed in DFs; blue horizontal lines: chosen |log2FC| > 1 cutoff. d Venn diagrams showing the overlap between RNA-Seq and CAGE-Seq and the identified LEC- (top) and BEC (bottom) core lncRNAs. LEC and BEC core lncRNAs are listed in Supplementary Data 2. e, f Pie charts showing the genomic classification according to FANTOM CAT database¹³ of LEC e and BEC f core lncRNAs compared to lncRNAs generally expressed in LECs or BECs by both RNA-Seq and CAGE-Seq (RNA-Seq: TPM > 0.5 and CAGE-Seq: CPM > 0.5).