Computational protocol: Functional diversity of CTCFs is encoded in their binding motifs

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Protocol publication

[…] To obtain the most reliable CTCF binding sites, we determined the binding sites by a combination of CTCF ChIP-seq data and motif scanning. Briefly, the peaks of CTCF ChIP-seq data were first called by MACS [] with threshold FDR < 0.01. Next, the gained peak regions were scanned by the three CTCF motif variations generated by our workflow (Fig. , Table ) using motif scan software FIMO []. Then, a CTCF binding site in the peak region was defined as the motif instance locus having a FIMO E-value < 0.01. Regions [−1500 bp, +1500 bp] centered at each CTCF binding motif were extracted and partitioned into 150 bins of 20 bp each. The signal strength of each bin was retrieved from the original ENCODE bigwig files (Additional file : Table S2). The fold-enrichment of a histone modification at each bin was defined as:Sij/CjWhere Sij is the strength of the i-th histone modification within the j-th bin, and Cj is the strength of Input in the j-th bin. […]

Pipeline specifications

Software tools BaMM!motif, MEME Suite
Application ChIP-seq analysis