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What is ChIP-seq?

This is a method to identify genome-wide DNA binding sites for a protein through combining chromatin immunoprecipitation with DNA sequencing. 

This method is mainly used to identify how chromatin associated proteins interact with DNA, influencing the gene expression. 

A. The wet lab workflow

  1. Cross-linking
  2. Chromatin fragmentation
  3.  Chromatin immunoprecipitation
  4. DNA recovery and purification
  5. Analysis by either  qPCR, ChIP-on-chip (hybrid array) or ChIP sequencing
B. Sequencing : 
C. Computational Analysis

Quality control

A quality control must be performed to ensure that the results are reliable. This should inlcude removing low-complexity regions because they do not provide any important information and could disrupt the mapping to the reference genome. In addition, attention should be paid to the ratio of reads located within each peak or lack of a peak. 

After this step, the reads are mapped to the reference genome. Then, peak calling is initated to detect genomic regions which are signifcantly enriched in ChIP reads. 

 

Peak calling

Peak calling methods are used to predict the DNA-bind sites from the read counts. Then, the density of reads can be observed across the genome. Each peak represents a possible candidate of histone modification and target protein or a DNA bind site. These peaks can be used to apply functional annotations.

Differential ChIP-seq analysis

To determine the differences between conditions. 

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