Visualized ChIP & ChIPseq protocol

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ChIP-seq (Chromatin Immunoprecipitation-and-Sequencing) has become a popular technique to find de novo and genome-wide binding sites of transcription factors. One of the basic yet laborious steps of this technique is the chromatin immunoprecipitation: If not even the positive control gives a signal after a 3-day experiment, and no mistake can be spotted in the preparation of the reagents or in following the steps of the protocol, most likely the protocol itself needs some optimization. Therefore, we usually prefer to use a protocol that has been established and evaluated already. However, this type of standard protocols sometimes fails to specify how exactly pipetting should be done, what size of the test tube should be used, what should be avoided during sonication etc. Thus, even with established protocols, these minor technical details can turn out to be crucial for a successful experiment. So, for ChIP, like for any bench experiment, we would seek help from an experienced lab mate. But getting someone to teach experiments, in particular these relatively novel techniques, whenever we need is not always easy. It might come as a great aid now that there is at least one journal that publishes not only the detailed protocol but also actually show how the experiment is performed in the laboratory. Since our collaborators in University of Illinois at Chicago (UIC) and ourselves are working in epigenetics and are performing ChIP-seq and ChIP routinely and successfully in the lab at UIC, we decided to visualize and publish one of the ChIP-seq experiments in the Journal of Visualized Experiments (JoVE). Also you can find the detailed protocol and the paper here. Hope this will help some of you who want to see a basic ChIP or ChIP-seq experiment in real time. I attach the video at the top of this post.