@article {563896, title = {ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.}, journal = {Genome Res}, volume = {22}, number = {9}, year = {2012}, month = {2012 Sep}, pages = {1813-31}, 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. }, keywords = {Animals, Chromatin Immunoprecipitation, Databases, Genetic, Genome, Genomics, Guidelines as Topic, High-Throughput Nucleotide Sequencing, Histones, Humans, Internet, Transcription Factors}, issn = {1549-5469}, doi = {10.1101/gr.136184.111}, author = {Landt, Stephen G and Marinov, Georgi K and Kundaje, Anshul and Kheradpour, Pouya and Pauli, Florencia and Batzoglou, Serafim and Bernstein, Bradley E and Bickel, Peter and Brown, James B and Cayting, Philip and Chen, Yiwen and DeSalvo, Gilberto and Epstein, Charles and Fisher-Aylor, Katherine I and Euskirchen, Ghia and Gerstein, Mark and Gertz, Jason and Hartemink, Alexander J and Hoffman, Michael M and Iyer, Vishwanath R and Jung, Youngsook L and Karmakar, Subhradip and Kellis, Manolis and Kharchenko, Peter V and Li, Qunhua and Liu, Tao and Liu, X Shirley and Ma, Lijia and Milosavljevic, Aleksandar and Myers, Richard M and Park, Peter J and Pazin, Michael J and Perry, Marc D and Raha, Debasish and Reddy, Timothy E and Rozowsky, Joel and Shoresh, Noam and Sidow, Arend and Slattery, Matthew and Stamatoyannopoulos, John A and Tolstorukov, Michael Y and White, Kevin P and Xi, Simon and Farnham, Peggy J and Lieb, Jason D and Wold, Barbara J and Snyder, Michael} }