ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.

He Q, Johnston J, Zeitlinger J. Nat Biotechnol. 2015;33:395-401.
Publication Notes: 
Accession number, availability of analysis code and experimental protocol All ChIP-nexus, ChIP-exo and ChIP-seq samples analyzed in this study are available from the NCBI Gene Expression Omnibus (GEO) under accession number GSE55306. All analysis code used for data processing and figure generation is available via GitHub at In addition, we have prepared a Linux virtual machine containing all software tools, analysis code, raw data and processed data used in this study. Instructions for accessing the virtual machine via Amazon Web Services, as well as a detailed ChIP-nexus protocol, can be found at our website (


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