For Chip-Seq library generation, in the size select step, I have had many problems using agarose; low resolution of short nucleotides and low % recovery using the min-elute columns. I prefer to use a TBE acrylamide gel. In order to do so, acrylamide gels electro-elution was employed, see Sambrook's molecular cloning. The problem with eletro-eluiton, in my hands, is that in the end I'm left with > 350ul of a dilute DNA solution. To use with Ampure beads, following the standard protocol, > 630ul of Ampure was required. This makes it an expensive step. I therefore have made an attempt to hack the kit. Please find attached the protocol I use and its companion excel spreadsheet. Archive.zip
I have used this protocol to purify 1ml 1ng/ul DNA sample with 10ul Ampure beads. I achieved ~40% recovery. This may save you 1 EtOH precipitation or save some of your Ampure XP.
I should add that standard column purification is easier and better suited for this type of application. However, Ampure XP has better size exclusion properties(removal of primers and adapter dimers). These properties make it well suited for ChIP-Seq library generation, in my opinion.
Please let me know about typos and mistakes.
I have used this protocol to purify 1ml 1ng/ul DNA sample with 10ul Ampure beads. I achieved ~40% recovery. This may save you 1 EtOH precipitation or save some of your Ampure XP.
I should add that standard column purification is easier and better suited for this type of application. However, Ampure XP has better size exclusion properties(removal of primers and adapter dimers). These properties make it well suited for ChIP-Seq library generation, in my opinion.
Please let me know about typos and mistakes.
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