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Old 12-03-2008, 06:41 PM   #1
Junior Member
Location: UK

Join Date: Jul 2008
Posts: 4
Default Discrepancies between PicoGreen and qPCR in GA libraries

Hi all GA users.
Some ChIP libraries we make are giving a ~4x lower concentration by qPCR compared to PicoGreen. These same libraries when sequenced generate low cluster number (~4x less than other libraries) which isnt increased by using a higher library concentration. The reads we get are high quality and sample DNA-specific. <2% of reads contain the adapter sequence GATCGGAAGA the libraries do not seem to contain the ~120bp adapter multimer band I have seen others comment on. Has anyone observed this sort of thing before or have a potential explanation of the cause? Thanks!
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