Hey people,

I am struggling since some months with a problem: I work with ChIP from liver tissue, and every time I have to check size on the agarose gel I always see a sharp band but not a smear!

The size of the band is correct but it is always a guessing if I smeared properly or not.

Usually is fine, but happened that I had a fragments around 1000bp that I did not see from the agarose gel and the ruined the whole experiment because noticed only when finishing the library prep.

I tried different dyes: Gel Red, Midori Green, EtBr pre and post staining. Only with the imager of another lab I obtained a good smear for the other cases no resolution at all.

In the first picture you see the first attempts where I also used the imager of another lab where I resolved the smear. On the second image you see another EtBr pre-stained gel visualised in a ChemiDoc and I cannot see the smear. I put already the filter for EtBr... so I do not know where the problem can be!

Do you have any clue? The agarose gel is around 2% in normal TE buffer without anything special. The samples are de cross linked and I am not sure is a preparation problem as on another imager I could see something!

Thanks!