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Does anyone know what the differences between the AMPure PacBio, AMPure XP or Illumina sample purification beads are? Different PEG concentrations,or if there no differences at all?
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AMPure XP beads and AMPure "PB" beads
AMPure "PB" beads are pre-washed AMPure XP beads. According to the document below from Pacific Biosciences, the AMPure XP beads have a contaminant that elutes simultaneously with your nucleic acids and may interfere with polymerase binding, especially in low quantities of DNA. The supernatant of the AMPure XP beads is replaced after washing the beads.
See page 16 of 67 in the pdf cited above for the recommended washes. Does anyone know what the contaminant is? I haven't contacted Beckman Coulter regarding this. -
Probably more important for PacBio, but azide is present (as a preservative), and that can affect polymerase activity.Comment
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Does anyone use brands of SPRI beads (such as MagBio's HighPrep PCR beads) rather than Beckman Coulter's Agencourt AMPure XP beads?Comment
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AMPure PB are specific formulation of AMPure XP for PacBio library clean ups and costs more than XP.Comment
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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
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