Problem with ligation using pJET and pGEM for clone library - (Jan/31/2013 )

I'm having again a similar problem. This time I get thousand of colonies in the transformation control, but no more than 20 colonies in the ligation control, as well as in the transformants with the inserts I want to clone.

I tried using pJET and a fresh kit of pGem T-easy cloning vector. Using the previous formula no longer fix my problems and tried ligation for pGem in1 hour at ambient T° up to 16 hours at 4°C, with no differences in results.

Why the ligation control does not work?

IS your competent cells fresh enough?

Are you cloning longer PCR fragment?

Also, check your fridge: I had seen a few labs where their faulty fridge (caused enzymes & ligases degrade over time) is the main reason of low efficiency.