用于定量检测小鼠肝组织中染色质可及性的批量和单细胞方案。

Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue.

机构信息

Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel.

Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.

出版信息

STAR Protoc. 2023 Sep 15;4(3):102462. doi: 10.1016/j.xpro.2023.102462. Epub 2023 Aug 16.

DOI:10.1016/j.xpro.2023.102462

PMID:37590150

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10440357/

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.

摘要

不同染色质区域对转录因子和其他 DNA 结合蛋白的可及性是细胞功能的一个关键决定因素。在这里，我们详细描述了一种改良的转座酶可及染色质测序（ATAC-seq）协议，该协议可以全面测量染色质可及性。我们描述了核分离、标签化、PCR 扩增以及测序前后的质量控制。我们的方案针对肝脏进行了优化，肝脏是一种需要独特步骤进行核分离的组织。我们提供了两个详细的示例：一个用于批量 ATAC-seq，另一个用于单细胞 ATAC-seq。