Brendo: an open resource for uniquely transcribed genes in brain endothelial cells

The blood-brain barrier (BBB) plays a critical role in central nervous system homeostasis, yet comprehensive transcrip- tional profiling of brain microvascular endothelial cells (BMECs) remains limited. Leveraging the increasing availability of publicly accessible bulk RNA sequencing (RNA-seq) datasets, we developed an integrated analytical framework to identify genes selectively enriched in BMECs compared to endothelial cells (ECs) from other tissues. To address the substantial batch effects inherent to multi-source bulk RNA-seq data, we combined two differential expression strate- gies, rank aggregation methods, and extensive quality controls. Our analysis incorporated EC samples from 16 different tissues and employed robust statistical workflows to mitigate technical confounders while preserving biologically mean- ingful signals. Validation using known BBB markers and independent proteomic evidence confirmed the reliability of our approach. We present Brendo (Brain Endothelial Open Resource), an open-access web platform providing searchable, filterable, and downloadable data on differentially expressed genes in BMECs. Brendo enables an in-depth exploration of brain endothelial gene expression and offers broader applications across vascular biology by supporting cross-tissue EC com- parisons. The workflow described is adaptable to other biological contexts, promoting the systematic reuse of public bulk RNA-seq datasets for target discovery. Collectively, this resource provides a foundation for advancing BBB-targeted therapeutic strategies and highlights the value of open data integration in transcriptomic research.