BulkECexplorer: a bulk RNAseq compendium of five endothelial subtypes that predicts whether genes are active or leaky

Abstract

AbstractTranscriptomic data obtained by single cell (sc) RNAseq or bulk RNAseq can be mined to understand the molecular activity of cell types. Yet, lowly expressed but functional genes may remain undetected in RNAseq experiments for technical reasons, such as insufficient read depth or gene drop out in scRNAseq assays. By contrast, bulk RNAseq assays may detect lowly expressed mRNA transcripts thought to be the biologically irrelevant products of leaky transcription. To more accurately represent a cell’s functional transcriptome, we propose compiling many bulk RNAseq datasets into a compendium and applying established classification models to predict whether the detected genes are likely active or leaky in that cell type. Here, we have created such a compendium for vascular endothelial cells from several mouse and human organs, termed the BulkECexplorer.