Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is the preferred approach to map histone modifications and identify cis-regulatory DNA elements throughout the genome. Multiple methods have been described to increase the efficiency of library preparation and to reduce hands-on time as well as costs. This review describes detailed steps to perform cell fixation, chromatin shearing, immunoprecipitation, and sequencing library preparation for a batch of 48–96 samples with small cell numbers. The protocol implements a semiautomated platform to reduce technical variability and improve signal-to-noise ratio as well as reduce hands-on time, thus allowing large-scale epigenetic studies of clinical samples with limited cell numbers.
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Acknowledgments
We thank the Vijayanand lab members for technical help and constructive discussions and Dr. Sharron Squazzo from Diagenode for technical assistance with the Bioruptor Pico and SX-8G IP-Star Compact machine and protocols. This work was supported by NIH grants (P.V.): NIH R24 AI108564, NIH U19 AI118626, NIH R01 HL114093, NIH R01 AI121426 and NIH S10 OD016262S10.
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Youhanna Jankeel, D., Cayford, J., Schmiedel, B.J., Vijayanand, P., Seumois, G. (2018). An Integrated and Semiautomated Microscaled Approach to Profile Cis-Regulatory Elements by Histone Modification ChIP-Seq for Large-Scale Epigenetic Studies. In: Reinhardt, R. (eds) Type 2 Immunity. Methods in Molecular Biology, vol 1799. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-7896-0_22
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DOI: https://doi.org/10.1007/978-1-4939-7896-0_22
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