In situ fixation and subsequent collection of cultured endothelial cells in a shear flow

Guilluy, 2014, Isolated nuclei adapt to force and reveal a mechanotransduction pathway in the nucleus, Nat. Cell Biol., 16, 376, 10.1038/ncb2927 Lovett, 2013, Modulation of nuclear shape by substrate rigidity, Cell. Mol. Bioeng., 6, 230, 10.1007/s12195-013-0270-2 Booth-Gauthier, 2012, Force-induced changes in subnuclear movement and rheology, Biophys. J., 103, 2423, 10.1016/j.bpj.2012.10.039 Tajik, 2016, Transcription upregulation via force-induced direct stretching of chromatin, Nat. Mater., 15, 1287, 10.1038/nmat4729 Lajoie, 2015, The Hitchhiker’s guide to Hi-C analysis: practical guidelines, Methods (San Diego, Calif.), 72, 65, 10.1016/j.ymeth.2014.10.031 Forcato, 2017, Comparison of computational methods for Hi-C data analysis, Nat. Methods, 14, 679, 10.1038/nmeth.4325 Belton, 2012, Hi-C: a comprehensive technique to capture the conformation of genomes, Methods (San Diego, Calif.), 58, 268, 10.1016/j.ymeth.2012.05.001 Baudin, 2007, A protocol for isolation and culture of human umbilical vein endothelial cells, Nat. Protoc., 2, 481, 10.1038/nprot.2007.54 Silva, 2018, A rapid extraction method for mammalian cell cultures, suitable for quantitative immunoblotting analysis of proteins, including phosphorylated GCN2 and eIF2α, MethodsX, 5, 75, 10.1016/j.mex.2017.10.008 Sapcariu, 2014, Simultaneous extraction of proteins and metabolites from cells in culture, MethodsX, 1, 74, 10.1016/j.mex.2014.07.002 Golloshi, 2018, Iteratively improving Hi-C experiments one step at a time, Methods, 10.1016/j.ymeth.2018.04.033 Lieberman-Aiden, 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science (New York, N.Y.), 326, 289, 10.1126/science.1181369 Belaghzal, 2017, Hi-C 2.0: an optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation, Methods, 123, 56, 10.1016/j.ymeth.2017.04.004 Tzima, 2005, A mechanosensory complex that mediates the endothelial cell response to fluid shear stress, Nature, 437, 426, 10.1038/nature03952 Davies, 1986, Turbulent fluid shear stress induces vascular endothelial cell turnover in vitro, Proc. Natl. Acad. Sci., 83, 2114, 10.1073/pnas.83.7.2114 Chiu, 2011, Effects of disturbed flow on vascular endothelium: pathophysiological basis and clinical perspectives, Physiol. Rev., 91, 327, 10.1152/physrev.00047.2009 DePaola, 1992, Vascular endothelium responds to fluid shear stress gradients, Arteriosclerosis Thrombosis: J. Vasc. Biol., 12, 1254, 10.1161/01.ATV.12.11.1254 Dewey, 1981, The dynamic response of vascular endothelial cells to fluid shear stress, J. Biomech. Eng., 103, 177, 10.1115/1.3138276 Illi, 2003, Shear stress–mediated chromatin remodeling provides molecular basis for flow-dependent regulation of gene expression, Circ. Res., 93, 155, 10.1161/01.RES.0000080933.82105.29 Dekker, 2002, Prolonged fluid shear stress induces a distinct set of endothelial cell genes, most specifically lung Krüppel-like factor (KLF2), Blood, 100, 1689, 10.1182/blood-2002-01-0046 Volger, 2007, Distinctive expression of chemokines and transforming growth factor-beta signaling in human arterial endothelium during atherosclerosis, Am. J. Pathol., 171, 326, 10.2353/ajpath.2007.061196 Lim, 2015, Culture and detection of primary cilia in endothelial cell models, Cilia, 4, 11, 10.1186/s13630-015-0020-2