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2006	3
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Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Mundade R, Ozer HG, Wei H, Prabhu L, Lu T. Mundade R, et al. Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201. Cell Cycle. 2014. PMID: 25486472 Free PMC article. Review.

Genome-Wide Identification of Transcription Factor-Binding Sites in Quiescent Adult Neural Stem Cells.

Mukherjee S, Hsieh J. Mukherjee S, et al. Methods Mol Biol. 2018;1686:265-286. doi: 10.1007/978-1-4939-7371-2_19. Methods Mol Biol. 2018. PMID: 29030827 Free PMC article.

Genome-wide epigenetic analysis of human pluripotent stem cells by ChIP and ChIP-Seq.

Hitchler MJ, Rice JC. Hitchler MJ, et al. Methods Mol Biol. 2011;767:253-67. doi: 10.1007/978-1-61779-201-4_19. Methods Mol Biol. 2011. PMID: 21822881

Characterization of genome-wide binding of NF-κB in TNFα-stimulated HeLa cells.

Xing Y, Yang Y, Zhou F, Wang J. Xing Y, et al. Gene. 2013 Sep 10;526(2):142-9. doi: 10.1016/j.gene.2013.05.001. Epub 2013 May 17. Gene. 2013. PMID: 23688556

An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.

Cheng CY, Chu CH, Hsu HW, Hsu FR, Tang CY, Wang WC, Kung HJ, Chang PC. Cheng CY, et al. BMC Genomics. 2014;15 Suppl 1(Suppl 1):S1. doi: 10.1186/1471-2164-15-S1-S1. Epub 2014 Jan 24. BMC Genomics. 2014. PMID: 24564277 Free PMC article.

Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data.

Zhang L, Xue G, Liu J, Li Q, Wang Y. Zhang L, et al. BMC Genomics. 2018 Dec 31;19(Suppl 10):914. doi: 10.1186/s12864-018-5278-5. BMC Genomics. 2018. PMID: 30598100 Free PMC article.

Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input.

Handa T, Harada A, Maehara K, Sato S, Nakao M, Goto N, Kurumizaka H, Ohkawa Y, Kimura H. Handa T, et al. Nat Protoc. 2020 Oct;15(10):3334-3360. doi: 10.1038/s41596-020-0375-8. Epub 2020 Aug 17. Nat Protoc. 2020. PMID: 32807906

Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.

Brdlik CM, Niu W, Snyder M. Brdlik CM, et al. Methods Enzymol. 2014;539:89-111. doi: 10.1016/B978-0-12-420120-0.00007-4. Methods Enzymol. 2014. PMID: 24581441

ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites.

Lefrançois P, Zheng W, Snyder M. Lefrançois P, et al. Methods Enzymol. 2010;470:77-104. doi: 10.1016/S0076-6879(10)70004-5. Epub 2010 Mar 1. Methods Enzymol. 2010. PMID: 20946807

Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by ChIP-seq.

Nielsen R, Mandrup S. Nielsen R, et al. Methods Enzymol. 2014;537:261-79. doi: 10.1016/B978-0-12-411619-1.00014-8. Methods Enzymol. 2014. PMID: 24480351

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