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Hello,
I am using two-color in SurePrint G3 Human Gene Expression 8x60K Microarray and wondering how many probes there is in one spot for one type of 60 nt sequence in length.
For instance, log-ratio tends to be approximately equal to zero (yellow spot after scaning slide) when the same sequence from two different samples are labeled with two different types of fluorescent dyes and bonds to it's complementary sequence printed in one spot. It's seems to be more then one probe in spot per sequence, but how many?
Thanks for any assistance
Exactly that what I am curious. So by "probe" meaning one probe per spot we do not know how many probe sequences are printed by company's printer on each spot. Even if we know that each measured spot is 30um width and 30um height and dsDNA have approximately 2.5 nm diameter we can not calculate how many ssDNA sequences of probe per spot are printed. Grateful for the prompt reply
No, you don't know how many DNA fragments there are in each spot, and there is no purpose in trying to compute it. The number differs between spots but is so astronomically large that, if the microarray is used properly, there are always more unhybridized fragments in each physical spot.
Thank you for explanation.