I had 96 PCR samples to run on gels today. It was a big experiment; a transfection time course with four different conditions and three different primer pairs.
And there appears to be something in the 8-tube strips I'm using that eats agarose, so the gels look like crap. Have a look at Figure 1.
See the shallow 'U'-shaped effect at the leading edge of the wells (arrowed)? That's making the bands themselves disperse. As I'm looking for small changes this is a bugger. I've been seeing it for a week or two now, ever since I started using this batch of 8-tube strips in fact, which makes me think it's something in or on the tube plastic.
Unfortunately the thermal cyclers (both of them. It might be time to suggest we acquire another one) are booked solid until Thursday so repeating the experiment is not going to happen quickly. I also don't think that there's much of a market for agarase.
(But despite all that, the experiment told me something useful. I can now distinguish between endogenous and transfected message. This is a good thing, and I might explain all later).
