Abstract
ChIP-seq is the current method of choice for genome-wide protein location analysis. Here, we present a native (non-cross-linked) ChIP procedure suitable for histone proteins, coupled with an efficient library preparation technique for subsequent next-generation sequencing. The method enables ChIP-seq starting with 50,000 or more cells.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dahl JA, Klungland A (2015) Micro chromatin immunoprecipitation (muChIP) from early mammalian embryos. Methods Mol Biol 1222:227–245
Dahl JA, Reiner AH, Collas P (2009) Fast genomic muChIP-chip from 1,000 cells. Genome Biol 10(2):R13
Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13(12):840–852
Ho JW, Bishop E, Karchenko PV et al (2011) ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics 12:134
Cao Z, Chen C, He B et al (2015) A microfluidic device for epigenomic profiling using 100 cells. Nat Methods 12(10):959–962
Rotem A, Ram O, Shoresh N et al (2015) Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol 33(11):1165–1172
Gilfillan GD, Hughes T, Sheng Y et al (2012) Limitations and possibilities of low cell number ChIP-seq. BMC Genomics 13:645
O'Neill LP, Turner BM (2003) Immunoprecipitation of native chromatin: NChIP. Methods 31(1):76–82
Thorne AW, Myers FA, Hebbes TR (2004) Native chromatin immunoprecipitation. Methods Mol Biol 287:21–44
Umlauf D, Goto Y, Feil R (2004) Site-specific analysis of histone methylation and acetylation. Methods Mol Biol 287:99–120
Sundaram AY, Hughes T, Biondi S et al (2016) A comparative study of ChIP-seq sequencing library preparation methods. BMC Genomics 17(1):816
Acknowledgment
G.D.G. is funded by the Norwegian South-Eastern Regional Health Authority. T.R. was funded by the EU-FP7 project EpiTrain (REA grant agreement n° 316758). We would also like to thank Diagenode for their support.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Ribarska, T., Gilfillan, G.D. (2018). Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers. In: Visa, N., Jordán-Pla, A. (eds) Chromatin Immunoprecipitation. Methods in Molecular Biology, vol 1689. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7380-4_14
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7380-4_14
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7379-8
Online ISBN: 978-1-4939-7380-4
eBook Packages: Springer Protocols