@article{83848b2af65442159a0826302c98e2eb,
title = "Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue",
abstract = "The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.",
keywords = "Genomics, Metabolism, Molecular Biology, Single Cell",
author = "Noga Korenfeld and Toft, {Nicolaj I.} and Dam, {Trine V.} and Meital Charni-Natan and Lars Gr{\o}ntved and Ido Goldstein",
note = "Funding Information: The methodology development in the Gr{\o}ntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant # 141 ). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907 ), the Israel Science Foundation (ISF, grants numbers 1469/19 , 3533/19 ), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing. Funding Information: The methodology development in the Gr{\o}ntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant #141). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907), the Israel Science Foundation (ISF, grants numbers 1469/19, 3533/19), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing. N.K. and N.I.T. developed and optimized the method and wrote the manuscript. T.V.D. and M.C-N. developed and optimized the method. L.G. and I.G. developed the method, acquired funding, supervised the project, and wrote the manuscript. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2023 The Author(s)",
year = "2023",
month = sep,
day = "15",
doi = "https://doi.org/10.1016/j.xpro.2023.102462",
language = "English",
volume = "4",
journal = "STAR Protocols",
issn = "2666-1667",
publisher = "Cell Press",
number = "3",
}