ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Name
Landt-2012-ChIP-seq guidelines.pdf
Size
2.58 MB
Format
Adobe PDF
Checksum (MD5)
0093e3a97baf4b9a7f5c33f8990c23bd
Author(s)
Kheradpour, Pouya
Kellis, Manolis
Date Issued
September 2012
Journal
Genome Research
Publisher
Cold Spring Harbor Laboratory Press
Citation
Landt, S. G. et al. “ChIP-seq Guidelines and Practices of the ENCODE and modENCODE Consortia.” Genome Research 22.9 (2012): 1813–1831.
Version
Final published version
Abstract
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 (http://www.modencode.org/) portals.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1101/gr.136184.111
