RT Journal
A1 Landt, Stephen G.
A1 Marinov, Georgi K.
A1 Kundaje, Anshul
A1 Kheradpour, Pouya
A1 Pauli, Florencia
A1 Batzoglou, Serafim
A1 Bernstein, Bradley E.
A1 Bickel, Peter
A1 Brown, James B.
A1 Cayting, Philip
A1 Chen, Yiwen
A1 DeSalvo, Gilberto
A1 Epstein, Charles
A1 Fisher-Aylor, Katherine I.
A1 Euskirchen, Ghia
A1 Gerstein, Mark
A1 Gertz, Jason
A1 Hartemink, Alexander J.
A1 Hoffman, Michael M.
A1 Iyer, Vishwanath R.
A1 Jung, Youngsook L.
A1 Karmakar, Subhradip
A1 Kellis, Manolis
A1 Kharchenko, Peter V.
A1 Li, Qunhua
A1 Liu, Tao
A1 Liu, X. Shirley
A1 Ma, Lijia
A1 Milosavljevic, Aleksandar
A1 Myers, Richard M.
A1 Park, Peter J.
A1 Pazin, Michael J.
A1 Perry, Marc D.
A1 Raha, Debasish
A1 Reddy, Timothy E.
A1 Rozowsky, Joel
A1 Shoresh, Noam
A1 Sidow, Arend
A1 Slattery, Matthew
A1 Stamatoyannopoulos, John A.
A1 Tolstorukov, Michael Y.
A1 White, Kevin P.
A1 Xi, Simon
A1 Farnham, Peggy J.
A1 Lieb, Jason D.
A1 Wold, Barbara J.
A1 Snyder, Michael
T1 ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
JF Genome Research 
JO Genome Research 
YR 2012 
FD September 01 
VO 22 
IS 9 
SP 1813 
OP 1831 
DO 10.1101/gr.136184.111 
UL http://genome.cshlp.org/content/22/9/1813.abstract 
AB 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.