TY  - JOUR
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
Y1  - 2012/09/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1813 
EP  - 1831 
DO  - 10.1101/gr.136184.111 
VL  - 22 
IS  - 9 
UR  - http://genome.cshlp.org/content/22/9/1813.abstract 
N2  - 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. 
ER  -