Chromatin immunoprecipitation assays for Myc and N-Myc

Bonnie L. Barrilleaux, Rebecca Cotterman, Paul S. Knoepfler

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Myc and N-Myc have widespread impacts on the chromatin state within cells, both in a gene-specific and genome-wide manner. Our laboratory uses functional genomic methods including chromatin immunoprecipitation (ChIP), ChIP-chip, and, more recently, ChIP-seq to analyze the binding and genomic location of Myc. In this chapter, we describe an effective ChIP protocol using specific validated antibodies to Myc and N-Myc. We discuss the application of this protocol to several types of stem and cancer cells, with a focus on aspects of sample preparation prior to library preparation that are critical for successful Myc ChIP assays. Key variables are discussed and include the starting quantity of cells or tissue, lysis and sonication conditions, the quantity and quality of antibody used, and the identification of reliable target genes for ChIP validation.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages117-133
Number of pages17
Volume1012
DOIs
StatePublished - 2013

Publication series

NameMethods in Molecular Biology
Volume1012
ISSN (Print)10643745

Fingerprint

Chromatin Immunoprecipitation
Sonication
Neoplastic Stem Cells
Antibodies
Genes
Libraries
Chromatin
Genome

Keywords

  • ChIP-seq
  • Chromatin immunoprecipitation
  • Epigenetics
  • Histone modifications
  • Myc
  • N-Myc

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Barrilleaux, B. L., Cotterman, R., & Knoepfler, P. S. (2013). Chromatin immunoprecipitation assays for Myc and N-Myc. In Methods in Molecular Biology (Vol. 1012, pp. 117-133). (Methods in Molecular Biology; Vol. 1012). https://doi.org/10.1007/978-1-62703-429-6-9

Chromatin immunoprecipitation assays for Myc and N-Myc. / Barrilleaux, Bonnie L.; Cotterman, Rebecca; Knoepfler, Paul S.

Methods in Molecular Biology. Vol. 1012 2013. p. 117-133 (Methods in Molecular Biology; Vol. 1012).

Research output: Chapter in Book/Report/Conference proceedingChapter

Barrilleaux, BL, Cotterman, R & Knoepfler, PS 2013, Chromatin immunoprecipitation assays for Myc and N-Myc. in Methods in Molecular Biology. vol. 1012, Methods in Molecular Biology, vol. 1012, pp. 117-133. https://doi.org/10.1007/978-1-62703-429-6-9
Barrilleaux BL, Cotterman R, Knoepfler PS. Chromatin immunoprecipitation assays for Myc and N-Myc. In Methods in Molecular Biology. Vol. 1012. 2013. p. 117-133. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-62703-429-6-9
Barrilleaux, Bonnie L. ; Cotterman, Rebecca ; Knoepfler, Paul S. / Chromatin immunoprecipitation assays for Myc and N-Myc. Methods in Molecular Biology. Vol. 1012 2013. pp. 117-133 (Methods in Molecular Biology).
@inbook{f2d3a35f2d1648ec9789ae2a51c8e5e7,
title = "Chromatin immunoprecipitation assays for Myc and N-Myc",
abstract = "Myc and N-Myc have widespread impacts on the chromatin state within cells, both in a gene-specific and genome-wide manner. Our laboratory uses functional genomic methods including chromatin immunoprecipitation (ChIP), ChIP-chip, and, more recently, ChIP-seq to analyze the binding and genomic location of Myc. In this chapter, we describe an effective ChIP protocol using specific validated antibodies to Myc and N-Myc. We discuss the application of this protocol to several types of stem and cancer cells, with a focus on aspects of sample preparation prior to library preparation that are critical for successful Myc ChIP assays. Key variables are discussed and include the starting quantity of cells or tissue, lysis and sonication conditions, the quantity and quality of antibody used, and the identification of reliable target genes for ChIP validation.",
keywords = "ChIP-seq, Chromatin immunoprecipitation, Epigenetics, Histone modifications, Myc, N-Myc",
author = "Barrilleaux, {Bonnie L.} and Rebecca Cotterman and Knoepfler, {Paul S.}",
year = "2013",
doi = "10.1007/978-1-62703-429-6-9",
language = "English (US)",
isbn = "9781627034289",
volume = "1012",
series = "Methods in Molecular Biology",
pages = "117--133",
booktitle = "Methods in Molecular Biology",

}

TY - CHAP

T1 - Chromatin immunoprecipitation assays for Myc and N-Myc

AU - Barrilleaux, Bonnie L.

AU - Cotterman, Rebecca

AU - Knoepfler, Paul S.

PY - 2013

Y1 - 2013

N2 - Myc and N-Myc have widespread impacts on the chromatin state within cells, both in a gene-specific and genome-wide manner. Our laboratory uses functional genomic methods including chromatin immunoprecipitation (ChIP), ChIP-chip, and, more recently, ChIP-seq to analyze the binding and genomic location of Myc. In this chapter, we describe an effective ChIP protocol using specific validated antibodies to Myc and N-Myc. We discuss the application of this protocol to several types of stem and cancer cells, with a focus on aspects of sample preparation prior to library preparation that are critical for successful Myc ChIP assays. Key variables are discussed and include the starting quantity of cells or tissue, lysis and sonication conditions, the quantity and quality of antibody used, and the identification of reliable target genes for ChIP validation.

AB - Myc and N-Myc have widespread impacts on the chromatin state within cells, both in a gene-specific and genome-wide manner. Our laboratory uses functional genomic methods including chromatin immunoprecipitation (ChIP), ChIP-chip, and, more recently, ChIP-seq to analyze the binding and genomic location of Myc. In this chapter, we describe an effective ChIP protocol using specific validated antibodies to Myc and N-Myc. We discuss the application of this protocol to several types of stem and cancer cells, with a focus on aspects of sample preparation prior to library preparation that are critical for successful Myc ChIP assays. Key variables are discussed and include the starting quantity of cells or tissue, lysis and sonication conditions, the quantity and quality of antibody used, and the identification of reliable target genes for ChIP validation.

KW - ChIP-seq

KW - Chromatin immunoprecipitation

KW - Epigenetics

KW - Histone modifications

KW - Myc

KW - N-Myc

UR - http://www.scopus.com/inward/record.url?scp=84884167523&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84884167523&partnerID=8YFLogxK

U2 - 10.1007/978-1-62703-429-6-9

DO - 10.1007/978-1-62703-429-6-9

M3 - Chapter

C2 - 24006062

SN - 9781627034289

VL - 1012

T3 - Methods in Molecular Biology

SP - 117

EP - 133

BT - Methods in Molecular Biology

ER -