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Old 02-21-2011, 01:23 AM   #1
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Location: Sweden

Join Date: Feb 2011
Posts: 3
Default ChIP seq - Different DNA size on agarosgel and Bioanalyzer

Dear all,

I'm performing chromatin imnmunoprecipitation and are shearing my crosslinked cells with a Bioruptor. After reverse crosslinking 65C, 5 h followed by DNA purification with E.Z.N.A cycle pure kit (column based) I analyze my Input chromatin (no IP) on a 1 % agarosgel and with Agilent DNA high sensitivity kit. The problem is that these two assays give totally different results. Agarosgel shows DNA library size of avarage 300 bp while bioanalyzer shows an avarage of 2500 bp?!?!

Which assay should I trust? What could be the reason for this difference?

See attached document.
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File Type: pdf agaros vs agilent DNA HS kit.pdf (90.8 KB, 72 views)
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