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==gDNA sample preparation== *Agilent protocol uses Preparing Samples for Paired-End Sequencing (Illumina), our protocol uses NEBNext DNA sample Prep Master Mix Set 1 (NEB, E6040S/L) #End-Repair reaction (blunt end sample with 3' phos.) #Qiagen Qiaquick column purification #Add βAβ Bases to the 3' end of the DNA fragments #Qiagen Qiaquick column purification #ligate the single-end adapters #Qiagen Qiaquick column purification (Ampure DNA purification kit can also be used) #amplify adapter-ligated samples #Qiagen Qiaquick column purification and PAGE gel verification *previous preparation steps can be found under labnotes 1-10-2010 for DF and foreskin sets *previous preparation steps can be found under labnotes 1-15-2010 for CViB and CViF sets *DF and foreskin sets still have purified post-PCR product after ligation *ligation step and beyond for CViB and CViF sets can be found under labnotes 2-15-10
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