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ChIP-exo

In the ChIP-exo simulation, you will perform the chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) protocol. Will you be able to prepare the target DNA to understand how E. coli survive in acid stress conditions?

About This 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 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, learning 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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Learning Objectives

  • Understanding the use of exonuclease treatment in ChIP-exo technique.
  • Learning 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.
  • Understanding the molecular mechanism of ChIP-exo.

Techniques

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

 

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