C versus TP

Looking at all the TP samples we have done so far in our experiment last night, I really wanted to figure out the difference between our saline samples and our toothpick samples. Today, I collected some cell samples using our old saline method (C) and the toothpick method (TP). After that, the samples are put under microscope for examination. Here are the taken pictures of the samples:

a) C sample:

b) TP sample:

Jonathan tried it later and got the same result. (I don’t have his pictures in my computer)

Obviously, there are differences between 2 samples. In the C  sampe, there are numerous free floating nuclei. On the other hands, the TP sample does not have any free floating nuclei. I suggest one hypothesis that our TP samples does not work because the DNA in these samples was not treated properly. Many DNA in the TP samples still stuck inside the cells (maybe the boiling process was not enough to lyse these cells). That is why the C samples, which have had more free floating nuclei already, are more likely to be ready for PCR than the TP sample.

Based on our observation in previous experiments, although many TP samples had much bigger pellet than the C samples, they did not work well (Even the HS Qubit Assay  we did early shows that TP samples had a very similar DNA concentration compared to the C samples). It proves that DNA quality plays a very important role here.Tomorrow, I will continue to check the affect of Chelex and heating to cells, nuclei, and DNA with microscope. I will also check the cells after heating at 57 Celsius  also. I will update this microscopic experiment as soon as possible.

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