RNA sequencing atlas of vascular endothelial cells

Work Group

Project Lead(s)

Project Status


Project Deliverable

O2-based RNA-seq pipeline

Collaborator Name

Ulrich von Andrian

HMS Department


Project Description

CCB worked with the von Andrian laboratory on a gene expression atlas of vascular endothelial cells based on RNA-sequencing (RNA-seq) of vascular bed samples of 20 murine tissues. CCB implemented (i) an O2-based RNA-seq pipeline that enabled efficient processing of raw sequencing output for 500 samples, (ii) statistical modeling for the identification of differentially expressed genes and gene sets, and (iii) an RStudioConnect interface consisting of different R/Shiny modules for visualization and interactive exploration of the different data layers. The implemented modules provide capabilities for exploring RNA-seq QC results, integrative exploration of gene expression levels and sample metadata, and exploration of alternative splicing, differential gene expression, and transcription factor activity enrichment within and across tissues.