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 ( 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