ChIP-exo Virtual Lab

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About the ChIP-exo Virtual Lab Simulation

In the ChIP-exo simulation, you will perform the chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) protocol in order to get a DNA sequence to elucidate the acid stress mechanism of Escherichia coli. You will learn how to fix the protein-DNA interactions and lyse the cells using a sonicator, add magnetic beads to the sample, and perform different on-bead and off-bead enzymatic modifications. From this, you will learn how the exonucleases work.

Will you be able to prepare the target DNA to understand how E. coli survive in acid stress conditions?

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Perform the chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) protocol, and prepare the target DNA to learn how E. coli survive in acid stress conditions.

Techniques In Lab

  • Cell lysis
  • Immunodetection
  • PCR
  • Sonication
  • Immunoprecipitation
  • DNA editing

 

Learning Objectives

At the end of this simulation, you will be able to…

  • Understand the use of exonuclease treatment in ChIP-exo technique.
  • Understand the key steps for performing the ChIP-exo technique as well as the importance of each reagent:
    • Adding formaldehyde to the culture to fix the bonds between proteins and DNA.
    • Lysing the cells using lysozyme and sonication.
    • Addition of specific antibodies.
    • Use of magnetic beads.
    • On-bead enzymatic modifications.
    • Off-bead enzymatic modifications.
  • Understand the molecular mechanism of ChIP-exo.

Screenshots of ChIP-exo Virtual Lab Simulation

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