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 dif...
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| Format: | Article |
| Language: | en_US |
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Cold Spring Harbor Laboratory Press
2013
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| Online Access: | http://hdl.handle.net/1721.1/77597 |
| _version_ | 1811095084119097344 |
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| author | Kheradpour, Pouya Kellis, Manolis |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Kheradpour, Pouya Kellis, Manolis |
| author_sort | Kheradpour, Pouya |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T16:10:03Z |
| format | Article |
| id | mit-1721.1/77597 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:10:03Z |
| publishDate | 2013 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/775972022-09-29T18:40:25Z ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia Kheradpour, Pouya Kellis, Manolis Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kheradpour, Pouya Kellis, Manolis 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. 2013-03-07T18:37:00Z 2013-03-07T18:37:00Z 2012-09 2011-12 Article http://purl.org/eprint/type/JournalArticle 1088-9051 http://hdl.handle.net/1721.1/77597 Landt, S. G. et al. “ChIP-seq Guidelines and Practices of the ENCODE and modENCODE Consortia.” Genome Research 22.9 (2012): 1813–1831. en_US http://dx.doi.org/10.1101/gr.136184.111 Genome Research Creative Commons Attribution Non-Commercial http://creativecommons.org/licenses/by-nc/3.0 application/pdf Cold Spring Harbor Laboratory Press Genome Research |
| spellingShingle | Kheradpour, Pouya Kellis, Manolis ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia |
| title | ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia |
| title_full | ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia |
| title_fullStr | ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia |
| title_full_unstemmed | ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia |
| title_short | ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia |
| title_sort | chip seq guidelines and practices of the encode and modencode consortia |
| url | http://hdl.handle.net/1721.1/77597 |
| work_keys_str_mv | AT kheradpourpouya chipseqguidelinesandpracticesoftheencodeandmodencodeconsortia AT kellismanolis chipseqguidelinesandpracticesoftheencodeandmodencodeconsortia |