Brash, James T; Diez-Pinel, Guillermo; Colletto, Chiara; Castellan, Raphael FP; Fantin, Alessandro; Ruhrberg, Christiana; (2024) The BulkECexplorer compiles endothelial bulk transcriptomes to predict functional versus leaky transcription. Nature Cardiovascular Research 10.1038/s44161-024-00436-w. (In press).

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Abstract

Transcriptomic data can be mined to understand the molecular activity of cell types. Yet, functional genes may remain undetected in RNA sequencing (RNA-seq) experiments for technical reasons, such as insufficient read depth or gene dropout. Conversely, RNA-seq experiments may detect lowly expressed mRNAs thought to be biologically irrelevant products of leaky transcription. To represent a cell type’s functional transcriptome more accurately, we propose compiling many bulk RNA-seq datasets into a compendium and applying established classification models to predict whether detected transcripts are likely products of active or leaky transcription. Here, we present the BulkECexplorer (bulk RNA-seq endothelial cell explorer) compendium of 240 bulk RNA-seq datasets from five vascular endothelial cell subtypes. This resource reports transcript counts for genes of interest and predicts whether detected transcripts are likely the products of active or leaky gene expression. Beyond its usefulness for vascular biology research, this resource provides a blueprint for developing analogous tools for other cell types.

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