Related Experiment Video
Updated: Jul 4, 2025
Gene Expression Analysis of Endothelial Cells Exposed to Shear Stress Using Multiple Parallel-plate Flow Chambers
Published on: October 21, 2018
Protocol for chromatin accessibility profiling of human endothelial cells cultured under fluid shear stress using
Lion Raaz1, Paul-Lennard Mendez2, Stefan Mundlos3
1Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; Institute of Medical and Human Genetics, Charité Universitätsmedizin, 13353 Berlin, Germany.
Abstract:
Chromatin accessibility influences gene regulation and can be quantified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Recapitulating in vivo fluid shear stress (FSS) mechano-regimes in vitro allows the study of atheroprone and atheroprotective mechanisms. In this protocol, we show how to culture and harvest endothelial cells from microfluidic channels for the preparation of ATAC-seq, highlighting optional growth factor stimulation and different FSS rates. This extends the application of ATAC-seq to the analysis of in vitro mechanically stimulated cells. For complete details on the use and execution of this protocol, please refer to Jatzlau et al.1.
