Abstract
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 language | English (US) |
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Journal | Methods in Enzymology |
DOIs | |
State | Accepted/In press - 2014 |
Keywords
- Acetylation
- ChIP-seq
- Chromatin
- Circadian
- Histone
- Methylation
- RNA polymerase II
- RNA-seq
- Sequencing
- Transcription
ASJC Scopus subject areas
- Biochemistry
- Molecular Biology