Questions related to summer 2014 research

2015-01-13

-What are the downs (down peptides)?  07-01-2014d1458 (after cancer meeting)
--Bart and Stephen think that the B cell that bound something matured away to make a new antibody that binds something else.  They think the up in normals may have common motifs with downs in disease.
-do the epitopes from the random peptides match well with anything in the frameshift database? 07-01-2014d1354 (after cancer meeting)
-do my pcr fusion transcripts have the same 1st transcript or 2nd transcript?  What is the exact identity of each part of the fusion?

-Why did some of the samples require more cycles and more template?
--Sample 350 and 399 with GF79 required more cycles or more template than sample 1228 and 1422 with GF60 and GF148.  Was this due to a different starting amount of template?
{
There wasn't conentration information for the cDNA, but here is the information for the RNA.
Sample	Concentration of the RNA (ng/uL)
350	2261
399	3097.9
1228	1104.2
1422	799.9
}
--The samples have the opposite concentrations that I would have expected.  I thought that sample 350 and 399 would have had the lower concentrations since they required more template.  With the evidence I have right now, I can't be sure if more cycles and template was required because the cDNA concentrations were different (only RNA concentrations are available) or because the different primers anneal differently and require more template or cycles.

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