ChIP实验仅仅是从样本中免疫沉淀富集特定目的DNA片段的过程，必须衔接下游实验才能得出有价值的结果。最常见的下游实验有四种：

1、标准PCR (ChIP-PCR)

用于定性检测、验证特定位点的组蛋白修饰水平或转录因子结合水平

示例结果图片如下：

ChIP下游常规PCR的电泳结果图

2、荧光定量PCR (ChIP-qPCR)

用于定量检测、验证特定位点的组蛋白修饰水平或转录因子结合水平。

示例结果图片如下（Input百分比分析法）：

ChIP下游荧光定量PCR的结果图

3、DNA微阵列芯片(ChIP-on-chip)

此方法已经基本被功能强大的二代测序所淘汰了。

4、二代测序(ChIP-Sequence)

用于全基因组范围内的筛选和发现全部位点的组蛋白修饰水平或转录因子结合水平。

示例结果图片如下：

ChIP-seq得到的信号峰peak在染色质上的分布谱

ChIP-seq得到的信号峰peak在染色质上的分布谱

ChIP-seq analysisshowing genome-wide distribution of SMC3 in trophozoites. (a) SMC3 distributionacross all 14 chromosomes. The blue box indicates the location of thecentromere on each chromosome. The regions depicted in (b) are indicated withblack boxes. (b) Zoomed in regions on chromosomes 2, 5 and 7 depicting SMC3distribution.

ChIP-sequence和RNA-sequence的联合分析

Correlation ofChIP-sequencing and RNA-sequencing data at the TBX2 and TBX4 loci. (A) Profilesof DNA sequence tag densities across the TBX2 and TBX4 loci followingChIP-sequencing with the indicated antibodies for BF and Hs68 cells. (B)Examples of duplicate RNA-sequencing analyses across the TBX2 and TBX4 loci forBF and Hs68 cells. kb, kilobase; RNA-seq, RNA-sequencing.

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