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NOTE: This page has ENCODE material from the the first production phase (completed Oct 2012). For current material, see the ENCODE Portal, encodeproject.org.
ENCODE Project at NHGRI Guidelines for Experiments

Current Guidelines:

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31.

ChIP-seq, ChIP-chip, DNase-seq, FAIRE-seq and DNAme Standards v2.0 (July 2011)

RNA Standards v1.0 (May 2011)

RIP Standards v2.0 (Jan 2012)

Antibody Characterization Standards (Feb 2014)

Previous Versions of Guidelines:

Cell Culture Guidelines

Chromatin and Transcription Factor Data Standards v1.0 (April 2010)

ChIP-seq Standards v1.0 ( Nov 2008)

DNase-seq and FAIRE-seq Standards (Jan 2009)

Standards for Data Reporting (Jan 2009)

Standards for Characterizing Histone Modification Antibodies (Nov 2008)

RNA-seq Best Practices (2009)

Updated 26 March 2014