Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.
Blacksburg High School, Blacksburg, Virginia 24060, United States.
Anal Chem. 2020 Oct 20;92(20):13661-13666. doi: 10.1021/acs.analchem.0c02550. Epub 2020 Oct 1.
Epigenome constitutes an important layer that regulates gene expression and dynamics during development and diseases. Extensive efforts have been made to develop epigenome profiling methods using a low number of cells and with high throughput. Chromatin immunoprecipitation (ChIP) is the most important approach for profiling genome-wide epigenetic changes such as histone modifications. In this report, we demonstrate microfluidic ChIPmentation (mu-CM), a microfluidic technology that enables profiling cell samples that individually do not generate enough ChIP DNA for sequencing library preparation. We used a simple microfluidic device to allow eight samples to be processed simultaneously. The samples were indexed differently using a tagmentation-based approach (ChIPmentation) and then merged for library preparation. A histone modification profile for each individual sample was obtained by demultiplexing the sequencing reads based on the indexes. Our technology allowed profiling 20 cells and is well suited for cell-type-specific studies using low-abundance tissues.
表观基因组构成了一个重要的调控层，调节着发育和疾病过程中的基因表达和动态。为了使用少量细胞并实现高通量来开发表观基因组分析方法，已经付出了广泛的努力。染色质免疫沉淀（ChIP）是分析组蛋白修饰等全基因组表观遗传变化的最重要方法。在本报告中，我们展示了微流控 ChIPmentation（mu-CM），这是一种微流控技术，可用于分析单个细胞样本，这些样本产生的 ChIP DNA 不足以用于测序文库制备。我们使用一个简单的微流控设备同时处理 8 个样本。使用基于标签酶切的方法（ChIPmentation）对样本进行不同的索引标记，然后合并进行文库制备。通过根据索引对测序reads 进行拆分，可以获得每个样本的组蛋白修饰图谱。我们的技术可以对 20 个细胞进行分析，非常适合使用低丰度组织进行细胞类型特异性研究。
