ChIP-seq Analysis

ChIP-seq (Chromatin Immunoprecipitation sequencing) is an NGS approach to identify protein-binding sites across the genome.  These proteins are most often transcription factors or histones, but could also be proteins involved in the transcription machinery.  Essentially, formaldehyde is used to crosslink and preserve protein-DNA interactions followed by chromatin shearing.  After immunoprecipitation of the protein of interest, crosslinking is reversed and the resulting DNA is sequenced and aligned to the reference genome, which identifies the locations within the genome where the protein had been bound.  Peaks can be identified that are significantly different between groups.

Deliverables

Differential Peaks: For each comparison, we provide a spreadsheet containing peaks that are significantly different.  Included in the spreadsheet is the log fold change in peak and the p-value.  This spreadsheet is annotated to include the feature on which the peak was found (promoter, UTR, intron, intergenic, etc), the nearest promoter and the nearest gene.

Motif Analysis: A motif analysis is an analysis tool that uses the DNA sequences of each identified peak and creates a consensus sequence, or multiple consensus sequences if the protein of interest is found to bind to multiple sequences.