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Ampure Xp Manual

I wanted to talk a little about the selection characteristics of Agencourt’s AMPure beads, a bead-reagent combination that purifies PCR reactions.

Agencourt Ampure Xp Kit

This stuff is incredible in terms of simplicity, efficiency, and high-throughput compatibility. I have a sneaking suspicion that AMPure, not unlike fire to Prometheus, was handed down from the gods to benefit humanity. You just dunk it into your sample, slosh it around, stick it to a magnet, wash, wash again, and elute in your favorite buffer. No muss, no fuss.

Beckman Ampure

We were wondering, though, about its selection process. What size fragments are selected by the AMPure beads, specifically at which ratio of beads to sample? So, like diligent scientists, we rolled up the sleeves of our labcoats and… read the protocol.

The protocol recommends washing your sample in a 1.8:1 ratio of beads to sample, although it says that fragments less than 100bp will be omitted at this ratio, it doesn’t say which sized fragments will be selected. We found this remarkably helpful technical bulletin, which describes calibrating each batch of AMPure beads with various ratios of DNA ladder.

AGENCOURT® RNACLEAN XP® Protocol 001298v001 Page 2 of 2 For questions regarding this protocol, call Technical Support at Agencourt 1-800-773-9186 Agencourt Bioscience Corporation, A Beckman Coulter Company 800-361-7780 978-867-2600 500 Cummings Center, Suite 2450 Beverly, Massachusetts 01915 www.agencourt.com. Consistently, 1% of sequencing reads from the Agencourt AMPure XP kit is smaller than 100 bp but nearly 5–10% of sequencing reads are smaller than 100 bp from column-based purification reagents (Additional file ). We tested whether purification reagents utilizing silica columns or SPRI may introduce any bias in ChIP-seq data.

Ampure

Ampure Xp Beads Manual

. Agencourt AMPure XP kit (Beckman Coulter, Cat. 17220600) All kits were also ranked from 1 (lowest) to 5 (highest) for ease of use based on the number of steps in the protocol, total time required, volume of binding buffer required, confidence regarding cross-contamination, and additional steps outside of the protocol. AMPure XP 5 mL reagent kit is a highly efficient, easily automated PCR purification system that delivers superior quality DNA with no salt carryover. Requiring no centrifugation or filtration, AMPure XP can be easily used in manual and automated 96- or 384-well formats. NC9959336 $415.40 / Each.

Ampure Xp Beads Manual

So I did our very own calibration with AMPure beads using Fermentas’s GeneRuler™ Low Range DNA Ladder (25-700 bp). I added 30ul ladder to various concentrations of AMPure beads according to Agencourt’s instructions.

Ampure Xp Beads Patent

(Actually, if you’re looking for good AMPure instructions, I recommend looking at Illumina’s TruSeq™ Sample Preparation Guide. Honestly, their instructions are more comprehensive than Agencourt’s, and easier to read.) After purifying each sample, I bookended the various AMPure:ladder ratios with 10ul non-purified ladder on a 2% TBE gel for easy comparison.

Ampure xp protocolAmpure

Beckman Coulter Ampure Xp

Without any further ado, here are the results: