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A small aliquot (1 µL) can be taken from the fragmentation product for analysis using electrophoresis-based methods [e.g., Bioanalyzer instrument (Agilent), TapeStation® system (Agilent)]. You can increase the reaction volume to 31 µL to compensate for this QC step. We have analyzed samples on an HS Bioanalyzer chip without cleanup (Figure). Migration is not affected but signal is reduced in samples run directly, without cleanup, when compared to samples with 1.8X SPRI cleanup.
Figure. Electrophoretic analysis of fragmentation samples with and without cleanup shows similar migration but lower signal without cleanup. Lotus DNA Library Prep libraries (150 ng input NA12878, Coriell; diluted to 5 ng/μL) with and without 1.8X SPRI cleanup were analyzed on a Bioanalyzer HS chip.