I'm in the process of cloning suspension cells and I need to use PCR for screening successful clones. What would be the easiest way to collect samples from 96-well plates, let's say about 5 to 10 cells from a well containing 20 to 30 cells in a volume of 100 ul? PCR seems to fail if I have more than 10 ul of cell culture medium in a 50 ul reaction volume, so I can't just suspend the cells in the whole volume and take a sample. I could use capillary to pick a few cells, but this would be quite tedious for large numbers of samples.
You can increase the PCR mix to 100 uL, take twice units Tag-polymerase, increase the number of cycles to 35-40. You can also try to add a PCR enhancer (5X KAPA Enhancer 1) of KAPA firm or the other. This enhancer significantly increases the amount of specific PCR product. http://www.kapabiosystems.com/products/name/kapa2g-robust-pcr-kits
I liked it. 5-10 cells should be sufficient for PCR. Check whether your culture medium contains of magnesium ions, if there is, re-calculate the concentration of Mg in the PCR mixture. Good luck. Excuse me for my English.
You can also try and do serial dilution from your culture medium. In this way you are both diluting the cells and whatever you have in the culture medium that affects your PCR
I know this is an old question, but...I would spin the plate and aspirate most of the medium with a multi-channel pipette.
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