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Old 03-29-2012, 02:25 PM   #1
ChristmasSunflower
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Location: US

Join Date: Mar 2009
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Default CHIP-Seq and MBDCap-Seq Library Prep

Hello,

We are working on both CHIP-Seq and MBDCap-Seq library preparation and sequencing now. I treat them as the similar type of partly genome enriched DNA. As you know, Illumina doesn’t have a CHIP-seq protocol that includes indexing, which really doesn't make a good sense for me. So we basically follow TruSeq DNA Sample Preparation Guide with the adjustment of primer concentration. Is this everyone who works with CHIP-Seq using now? We use 16 PCR cycles for the enrichment of library.

I'm a kind of confused why CHIP-Seq protocol just uses as little as 10ng starting enriched DNA, in comparison with TruSeq DNA protocol. Does anyone here have good experience on the low starting materials? I will appreciate if you know MBDCap-Seq library preparation and like to share your experience here.

Thanks!
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