CORY was actually pre-selected for us. However, it was a good gene to study because of it’s gene profile. As I explained in the poster, the gene expression profile for rad51, a gene that is known to increase in expression during dna damage, is very similar to the gene expression profile of cory.
There’s a few things that may have happened. Most likely, the primer designed for figure (1) was not suitable. We designed the primers using an online tool and looked for characteristics that would be ideal for the experiment, but it did not end up working. The primer for figure (2), however, was validated by other lab members, so it’s especially interesting that this one didn’t work (considering the fact that rad51 and rpp0 showed up nicely). I think it’s possible that the primers had degraded by the end of the semester, even though this is not likely. Good question!
As stated above, the primer designed in figure one probably had some dysfunction that we did not account for. The online tool (primer3plus) is pretty good for designing primers, but sometimes primers don’t work despite of the primer hypothetically being a ‘good fit’. The primer for figure 2, however, annealed when used by other people in our lab. This means that primer 2 not annealing is most likely due to a degraded primer/human error.
Although it’s unlikely that a primer will anneal during qpcr if it didn’t for the type of pcr that we did, the way that data is generated for qpcr is different. Instead of running a gel, the data is usually shown in the form of a graph. This, compared to quantifying the ‘brightness’ of our pcr bands, is more quantitative data and could increase the quality of our results.
curesymposium.org 
Were there any other genes you considered for this experiment, and if so, why did you ultimately choose the gene you did?
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CORY was actually pre-selected for us. However, it was a good gene to study because of it’s gene profile. As I explained in the poster, the gene expression profile for rad51, a gene that is known to increase in expression during dna damage, is very similar to the gene expression profile of cory.
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Why didn’t the primer anneal?
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There’s a few things that may have happened. Most likely, the primer designed for figure (1) was not suitable. We designed the primers using an online tool and looked for characteristics that would be ideal for the experiment, but it did not end up working. The primer for figure (2), however, was validated by other lab members, so it’s especially interesting that this one didn’t work (considering the fact that rad51 and rpp0 showed up nicely). I think it’s possible that the primers had degraded by the end of the semester, even though this is not likely. Good question!
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why didn’t the primer work?
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As stated above, the primer designed in figure one probably had some dysfunction that we did not account for. The online tool (primer3plus) is pretty good for designing primers, but sometimes primers don’t work despite of the primer hypothetically being a ‘good fit’. The primer for figure 2, however, annealed when used by other people in our lab. This means that primer 2 not annealing is most likely due to a degraded primer/human error.
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How would Q PCR be able to help to gain data?
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Although it’s unlikely that a primer will anneal during qpcr if it didn’t for the type of pcr that we did, the way that data is generated for qpcr is different. Instead of running a gel, the data is usually shown in the form of a graph. This, compared to quantifying the ‘brightness’ of our pcr bands, is more quantitative data and could increase the quality of our results.
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