ATAC-Seq Analysis of Accessible Chromatin: From Experimental Steps to Data Analysis.
ATAC-Seq Analysis of Accessible Chromatin: From Experimental Steps to Data Analysis.
复制标题
可访问染色质的 ATAC-Seq 分析：从实验步骤到数据分析。
DOI：
10.1007/978-1-0716-2724-2_5
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Maezawa,So
中科院分区：
文献类型：
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作者：
Tatara,Mayu;Ikeda,Taiyo;Namekawa,SatoshiH;Maezawa,So
可染色质通常代表基因表达所必需的基因调控元件，包括启动子和增强子。转座酶可重复染色质测序（ATAC-seq）是研究染色体可及性的最常用技术之一。在这里，我们逐步描述了一系列优化的实验方法和ATAC-seq分析的生物信息学管道。作为一个例子，我们提出了一种分析小鼠生精细胞：一种方法来分离生殖细胞，一个反应步骤，使用Tn 5转座酶插入测序接头到可访问的DNA，高通量测序的文库制备方法，和测序数据的生物信息学分析。总的来说，我们介绍了一个框架的ATAC-seq分析，可以应用于任何细胞群体，以确定细胞类型特异性基因调控元件和它们的顺式调控网络。
Accessible chromatin often represents gene regulatory elements, including promoters and enhancers, essential for gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is one of the most popular techniques to investigate chromatin accessibility across the genome. Here we describe, step by step, a series of optimized experimental methods and bioinformatics pipelines for ATAC-seq analysis. As an example, we present an analysis of murine spermatogenic cells: a method to isolate germ cells, a reaction step using Tn5 transposase to insert sequencing adapters into accessible DNA, a library preparation method for high-throughput sequencing, and bioinformatics analysis of sequencing data. Overall, we introduce a framework of ATAC-seq analysis that can be applied to any cell population to identify cell-type-specific gene regulatory elements and their cis-regulatory networks.