热带爪蟾和非洲爪蟾的染色质免疫沉淀及深度测序
Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis.
作者信息
Wills Andrea E, Gupta Rakhi, Chuong Edward, Baker Julie C
机构信息
Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA.
出版信息
Methods. 2014 Apr 1;66(3):410-21. doi: 10.1016/j.ymeth.2013.09.010. Epub 2013 Sep 21.
Abstract
Chromatin immunoprecipitation and deep sequencing (ChIP-SEQ) represents a powerful tool for identifying the genomic targets of transcription factors, chromatin remodeling factors, and histone modifications. The frogs Xenopus laevis and Xenopus tropicalis have historically been outstanding model systems for embryology and cell biology, with emerging utility as highly accessible embryos for genome-wide studies. Here we focus on the particular strengths and limitations of Xenopus cell biology and genomics as they apply to ChIP-SEQ, and outline a methodology for ChIP-SEQ in both species, providing detailed strategies for sample preparation, antibody selection, quality control, sequencing library preparation, and basic analysis.
摘要
染色质免疫沉淀与深度测序（ChIP-SEQ）是一种强大的工具，可用于识别转录因子、染色质重塑因子和组蛋白修饰的基因组靶点。非洲爪蟾和热带爪蟾一直是胚胎学和细胞生物学领域杰出的模型系统，作为全基因组研究中极易获取的胚胎，其应用价值也日益凸显。本文重点探讨了爪蟾细胞生物学和基因组学在应用于ChIP-SEQ时的特殊优势和局限性，并概述了两种爪蟾物种的ChIP-SEQ方法，提供了样本制备、抗体选择、质量控制、测序文库制备和基础分析的详细策略。
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