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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?
Thanks
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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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