BBBomics – Human Blood Brain Barrier Transcriptomics Hub

Blood-brain barrier (BBB) is a monolayer of endothelial cells that line brain capillaries. The BBB protects brain by blocking the entry of harmful substances from blood and shielding the brain from peripheral fluctuations in hormones, fatty acids, and electrolytes. In addition, the BBB effectively clears brain metabolites and serves as a major conduit for the delivery of crucial nutrients and growth factors needed for proper brain function.

Next-generation sequencing technology unveils the full potential of systems biology approaches to resolve cellular and molecular interaction networks that regulate the functional integrity of the BBB. Such a panoramic view of the interaction networks could enable us to isolate key players regulating a physiological process and investigate how they are affected in various diseases.

Researchers from the Mayo Clinic Rochester are the first to generate deep RNA sequencing and microRNA sequencing of a human BBB cell line. BBBomics hub is a comprehensive portal for BBB transcriptomics data, obtained by sequencing mRNA (mRNA-seq) and microRNA (miRNA-seq) of polarized hCMEC/D3 cell monolayers. This data encompasses coding (gene expression, alternate splice forms, expressed single nucleotide variants -eSNVs) and non-coding (microRNA, LincRNA, circular RNA) counts that are easily accessible through BBBomics hub database. The researhers also superimposed the RNA-seq coding data on 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which include canonical, non-canonical, and/or atypical pathways retrievable using BBBomics hub.

Example pathway (Alzheimer’s disease) overlaid with gene expression data from BBB cell line.


The pathway consists of a snapshot of genes expression profiles in replicate cultures of hCMEC/D3 cell lines.

Availability – The data is easily accessible and freely available at

Kalari KR, Thompson KJ, Nair AA, Tang X, Bockol MA, Jhawar N, Swaminathan SK, Lowe VJ, Kandimalla KK. (2016) BBBomics-Human Blood Brain Barrier Transcriptomics Hub. Front Neurosci 10:71. [article]

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