Long Jiaxin, Johnson Emily T, Ogas Joe
Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
Methods Mol Biol. 2025;2919:179-198. doi: 10.1007/978-1-0716-4486-7_10.
ChIP-seq is a commonly used method to characterize chromatin-associated features on a genome-wide basis. A common set of steps for a ChIP-seq procedure prior to sequencing includes crosslinking, nuclei extraction, chromatin shearing, immunoprecipitation, elution, reversal of crosslinks, and library preparation. Plant material can be challenging to process for ChIP-seq analysis due to the unique attributes of plant cells that impair success. Here, we describe an effective ChIP-seq sample preparation method that is optimized for generating robust libraries from complex plant materials. In particular, we identify time as a critical parameter for effective coupling of ChIP-seq sample preparation with a commercially available kit to generate robust NGS libraries in-house. The resulting protocol is a cost-effective strategy to generate reliable ChIP-seq libraries from complex plant material and thereby acquire representative sequencing data.
染色质免疫沉淀测序（ChIP-seq）是一种常用于在全基因组范围内表征与染色质相关特征的方法。测序前ChIP-seq程序的一组常见步骤包括交联、细胞核提取、染色质剪切、免疫沉淀、洗脱、交联逆转和文库制备。由于植物细胞的独特属性会影响ChIP-seq分析的成功率，因此处理植物材料进行ChIP-seq分析具有挑战性。在此，我们描述了一种有效的ChIP-seq样本制备方法，该方法经过优化，可从复杂的植物材料中生成可靠的文库。特别是，我们确定时间是将ChIP-seq样本制备与市售试剂盒有效结合以在内部生成可靠的二代测序（NGS）文库的关键参数。所得方案是一种经济高效的策略，可从复杂的植物材料中生成可靠的ChIP-seq文库，从而获得具有代表性的测序数据。
