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

Overview

Journal Methods Enzymol

Specialty Biochemistry

Date 2015 Feb 10

PMID 25662462

Citations 18

Authors

Joseph S Takahashi

Vivek Kumar

Prachi Nakashe

Nobuya Koike

Hung-Chung Huang

Carla B Green

Tae-Kyung Kim

Affiliations

Soon will be listed here.

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.

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