ChIP-seq and RNA-seq Methods to Study Circadian Control of Transcription in Mammals

Joseph S. Takahashi, Vivek Kumar, Prachi Nakashe, Nobuya Koike, Hung Chung Huang, Carla B. Green, Tae Kyung Kim

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Genome-wide analyses have revolutionized our ability to study the transcriptional regulation of circadian rhythms. The advent of next-generation sequencing methods has facilitated the use of two such technologies, ChIP-seq and RNA-seq. In this chapter, we describe detailed methods and protocols for these two techniques, with emphasis on their usage in circadian rhythm experiments in the mouse liver, a major target organ of the circadian clock system. Critical factors for these methods are highlighted and issues arising with time series samples for ChIP-seq and RNA-seq are discussed. Finally, detailed protocols for library preparation suitable for Illumina sequencing platforms are presented.

Original languageEnglish (US)
JournalMethods in Enzymology
StateAccepted/In press - 2014


  • Acetylation
  • ChIP-seq
  • Chromatin
  • Circadian
  • Histone
  • Methylation
  • RNA polymerase II
  • RNA-seq
  • Sequencing
  • Transcription

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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