Journal: Nucleic Acids Research
Article Title: PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond
Figure Lengend Snippet: From the input treated CTCF ChIP-exo data set, ( A ) read tag distributions around all genomic CTCF-bound sites shown in the four binned motif combinations (right panel) were centered on the midpoint of the CTCF consensus to generate a heat map (top left) which is summed below as an aggregate plot. Denoted in blue and red are the sense and antisense strand read enrichments around the core CTCF motif, respectively. The centralized CTCF core sequence and adjacent motifs are depicted above a color map representation of 50 bp DNA stretches containing the various motif combinations (right panel). ( B ) Heat maps from RNA-seq data depicting gene transcripts exhibiting a two-fold up- (green) or down-regulation (red) after CTCF depletion relative to the scrambled siRNA control (Scr). For each motif group, CTCF promoter occupation sites (defined as ±1000 bps around the transcription start site (TSS)) were intersected with the RNA-seq data and resulting altered gene sets were binned as individual heat maps. ( C ) Each gene set from ( B ) was subjected to Ingenuity Pathway Analysis (IPA, www.ingenuity.com ) to identify biological pathways uniquely modulated by each of the CTCF motif combinations. ( D–F ) The same analyses in ( A–C ) were performed separately on the core CTCF consensus with the newly identified 3′-CTCF motif.
Article Snippet: Once covalently bound to the magnetic beads, the input samples were treated identically as described above for the CTCF ChIP-exo samples utilizing reagents and materials from the Active Motif ChIP-exo Kit.
Techniques: Chromatin Immunoprecipitation, Sequencing, RNA Sequencing Assay, Indirect Immunoperoxidase Assay