Computational protocol: FOXA1 is a critical determinant of Estrogen Receptor function and endocrine response

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Protocol publication

[…] ChIP DNA was amplified as previously described. Sequences generated by the Illumina GAIIx genome analyzer (using 36bp reads) were aligned against NCBI Build 36.3 of the human genome using MAQ (http://maq.sourceforge.net/) with default parameters. For each biological replicate, a corresponding set of Input sequence reads of similar size was obtained by random sampling from the full set of Input sequence reads. Peaks were called using Model-based Analysis for ChIP-Seq (MACS), run using default parameters. […]

Pipeline specifications

Software tools MAQ, MACS
Application ChIP-seq analysis
Diseases Breast Neoplasms
Chemicals Estrogens, Tamoxifen