Any help on this is appreicated.
I constructed Solexa ChIP-Seq libraries for yeast (S. cerevisiae). As the quantity of the ChIP DNA from 320 ml yeast culture was very low, I did PCR before size selection. However, the gel purified DNA showed no peak at expected size by Agilent DNA 1000 chip measurement. I suspect that it's because the DNA quantity was too low to show.
The PCR I did was according to Illumina's standard protocol: primer 1.1 and 2.1, 1 μl each; total volume 50 μl; 18 cycles.
Any advice, except increasing the volume of original yeast culture, would be helpful.
P.s. Is the concentration of primers 1.1 and 2.1 supplied by Illumina 10 μM?
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