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 language | English (US) |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Pages | 117-133 |
| Number of pages | 17 |
| Volume | 1012 |
| DOIs | |
| State | Published - 2013 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 1012 |
| ISSN (Print) | 10643745 |
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Keywords
- ChIP-seq
- Chromatin immunoprecipitation
- Epigenetics
- Histone modifications
- Myc
- N-Myc
ASJC Scopus subject areas
- Molecular Biology
- Genetics
Cite this
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 proceeding › Chapter
}
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 -