1. 2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells.
- Author
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Hu, Congxia, Wu, Jun, Li, Pengxiao, Zhang, Yabin, Peng, Yonglin, Liu, Ruiqi, Du, Wenfei, Kang, Yani, Sun, Jielin, Wu, Ji, Shao, Zhifeng, and Zhao, Xiaodong
- Subjects
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STEM cells , *DNA methylation , *NUCLEOTIDE sequencing , *HISTONES , *GERM cells , *DNA - Abstract
Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) can profile genome-wide epigenetic marks associated with regulatory genomic elements. However, conventional ChIP-seq is challenging when examining limited numbers of cells. Here, we developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during conventional ChIP procedures (hereafter referred to as 2cChIP-seq), thus dramatically improving immunoprecipitation efficiency and reducing DNA loss of low-input ChIP-seq samples. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10–1000 cells. By introducing Tn5 transposase-assisted fragmentation, 2cChIP-seq reliably captured genomic regions with histone modification at the single-cell level in about 100 cells. Moreover, we characterized the methylome of 100 differentiated female germline stem cells (FGSCs) and observed a particular DNA methylation signature potentially involved in the differentiation of mouse germline stem cells. Hence, we provided a reliable and robust epigenomic profiling approach for small cell numbers and single cells. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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