ChIPmentation: fast, cheap, low-input ChIP-seq for histones and transcription factors

Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is widely used to map histone marks and transcription factor binding throughout the genome. Here we present ChIPmentation, a method that combines ChIP with sequencing library preparation by Tn5 transposase (“tagmentation”). ChIPmentation introduces sequencing-compatible adapters in a single-step reaction directly on bead-bound chromatin, which reduces time, cost, and input requirements, making ChIPmentation a convenient and high-throughput alternative to existing ChIP-seq protocols. Overall design: This submission includes sequencing data for 87 samples: 52 ChIPmentation and 24 ChIP-seq for 10 different antibodies with at least two biological replicates each and matched immunoglobulin controls in the majority of cases; 2 ATAC-seq samples were sequenced for comparison; Additionally, 9 samples of a experimental protocol which we called “ChIP-tagmentation” were produced without replication.

染色质免疫共沉淀结合下一代测序（ChIP-seq）是当前广泛用于全基因组组蛋白修饰位点与转录因子结合区域定位分析的技术。本研究介绍了ChIPmentation技术：该方法将染色质免疫共沉淀（ChIP）与Tn5转座酶介导的测序文库制备步骤（即"tagmentation（转座标记）"）相结合。ChIPmentation可直接在磁珠结合的染色质上通过单步反应引入适配于测序的接头序列，从而缩短实验周期、降低成本并减少样本起始量需求，使其成为现有ChIP-seq实验方案中便捷且高通量的替代方案。实验整体设计如下：本次提交包含87份样本的测序数据：其中52份为ChIPmentation测序数据、24份为ChIP-seq测序数据，覆盖10种不同抗体，每类抗体至少设置2次生物学重复，且绝大多数组别均配有匹配的免疫球蛋白对照；此外还设置2份ATAC-seq（转座酶可及性测序）样本用于对照分析；另有9份采用我们命名为"ChIP-tagmentation"的实验方案制备的样本，未设置生物学重复。