Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis.
Chromatin immunoprecipitation and deep sequencing (ChIP-SEQ) represents a powerful tool for identifying the genomic targets of transcription factors, chromatin remodeling factors, and histone modifications. The frogs Xenopus laevis and Xenopus tropicalis have historically been outstanding model systems for embryology and cell biology, with emerging utility as highly accessible embryos for genome-wide studies. Here we focus on the particular strengths and limitations of Xenopus cell biology and genomics as they apply to ChIP-SEQ, and outline a methodology for ChIP-SEQ in both species, providing detailed strategies for sample preparation, antibody selection, quality control, sequencing library preparation, and basic analysis.
Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Andrea E
AE
Wills
Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Rakhi
R
Gupta
Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Edward
E
Chuong
Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA. Electronic address: jbaker@stanford.edu.
Julie C
JC
Baker
D000818:Animals; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D014981:Xenopus / Q000235:genetics*
ChIP-SEQ; Chromatin immunoprecipitation; Embryo; Xenopus laevis; Xenopus tropicalis