Jie:LabNotes/CpgSeq/2009-6-19
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set up the suppressor oligo
the average concentration of cpg97k probe is ~20ng/ul (~600nM).The volume of probe in a 10ul capture reaction is 2.5ul. The mole ratio of suppressor oligo: probe is 100:1. So the suppressor oligo concentration in a 10ul capture reaction should be: ((600nM*2.5)/97k)*100=1.5nM. I prepared the 100x suppressor oligo as 150nM/each, then dilute to 10x working mixture. I adjusted the concentration of oligoes according to their read abundance.
For cpg55B subset, the read abundance range from 430-1673. The oligo(50uM) volume used is 0.5ul/each. The final volume of mixture = (50uM*0.5ul)/150nM = 180ul. So I take 0.5ul oligo (50uM)/each and added ddH2O to get the final volume of 180ul.
For cpg55A subset, I adjusted the ration according to the abundance range. A1-E1: take 5ul/oligo; F1-H1: take 3ul/oligo; A2-H3: take 1ul/oligo; A4-H12: take 0.5ul/oligo; add ddH2O to get the final volume of 180ul.