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Published September 2012 | Published + Supplemental Material
Journal Article Open

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia


Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE.

Additional Information

© 2012 Cold Spring Harbor Laboratory Press. Received December 10, 2011; accepted in revised form May 10, 2012. We thank the ENCODE and modENCODE project consortia for helpful discussions and making their data available. We also thank Elise Feingold, Peter Good, and Kevin Struhl for advice and helpful discussions, and Leslie Adams and Caroline Kelly for help in preparing the manuscript.

Attached Files

Published - Genome_Res.-2012-Landt-1813-31.pdf

Supplemental Material - SuppLegends.docx

Supplemental Material - Supp_Fig_S1.tif

Supplemental Material - Supp_Fig_S2.tif

Supplemental Material - Supp_Fig_S3.tif


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August 19, 2023
October 19, 2023