Low quantity of ChIP DNA- Advice?

Quest · 01-29-2009, 10:51 PM

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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01-29-2009, 10:51 PM	#1
Quest Junior Member Location: singapore Join Date: May 2008 Posts: 3	Low quantity of ChIP DNA- Advice? 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?