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Optimizing ChIP for Reproducibility

Dr. Hamid Khoja

Chromatin Immunoprecipitation (ChIP) is a powerful technique for evaluating the interactions
of proteins with specific regions of genomic DNA, helping to better understand the mechanisms
such as, gene regulation, DNA replication, repair and recombination, and epigenetic silencing.
The use of ChIP in conjunction with NGS (ChIP-Seq) has enabled wide scale application of this
technique to ascertain genome wide DNA binding sites. However, sample preparation for ChIP
and ChIP-seq has multiple steps which are critical to the success of the experiments and affect
the reproducibility, bias, and sensitivity of the technique.

Successful ChIP experiments demand chromatin that is sheared to manageable fragments sizes
while retaining the integrity of the DNA, preserving protein epitopes and the formaldehyde
cross-links attaching the proteins of interest to the DNA to deliver sensitive and reproducible
results. Current methods for shearing chromatin to the desired size for immunoprecipitation in
ChIP experiments are a source of significant imprecision, adversely affecting the reproducibility
of ChIP experiments. In this webinar, scientist from Covaris will discuss how to better optimize
your sample preparation to improve the reproducibility of your results and present data
demonstrating how Covaris’ AFA Technology is ideally suited to provide the highest quality
sheared chromatin. Shearing chromatin with AFA preserves precious epitopes, maintains DNA
quality, protects from shearing biases, and provides highly reproducible results which are the
reasons AFA is quickly becoming the standard chromatin shearing solution in leading epigenetic