Washing procedure in ChIP-exo

The washing procedure in ChIP-exo is very simple. It uses four different buffers (I, II, III and IV) with gradual salt concentrations that will allow the removing of unwanted compounds on the mixing and at the same time preserving the antibody coupled protein-DNA complexes.

Each washing procedure has the same steps:

1. Pull down the magnetic beads using the magnetic rack.

2. Remove the solution from the tube when all the beads are attached to the magnet (a pellet will be visible on the side of the tube).

3. Place the tube in a normal rack and resuspend with washing buffer I

4. Place the tube back in the magnetic rack to pull down the beads again.

Repeat steps 1-4 once for buffer I, and then repeat them again using buffer II, III and IV.

In order to not lose final yield, it's also important to follow the next tips:

• Make sure that you remove all the residual buffer on the inner side of the tube cap by using vacuum.

• When resuspending the sample in washing buffers, pipette the mix up and down to avoid the formation of bubbles.

• Do not vortex any samples while beads are bound to the tagged protein. It may cause antibody detachment from the beads.

• When washing with buffer IV (TE buffer), first, take out most of the supernatant by pipetting and then suck out the residual completely by vacuum.