Author Archives: Kristin

Home Made AMPure XP Beads

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AMPure XP beads are used to quickly clean PCR reactions and are also used in WGS library prep. You can also use them to do DNA size selections! They work well, but are very expensive. I found step-by-step instructions on how to make a home-made version online, purchased the reagents and tried the protocol. I tested the beads by attempting to clean up DNA ladder and I found that the home-made beads work identically to the AMPure XP beads.

Attached is the protocol for making the beads. I followed the protocol exactly. One note, I weighed the PEG-8000 in the fume hood because the fine powder is an irritant if inhaled. I also have attached a picture of my gel comparing clean-up of 100 bp DNA ladder with commercial AMPure XP beads and the home-made substitute.

Home-Made AMpure XP beads

AMPure clean-up comparison

Bioanalyzer – RNA (Kristin)

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Running a RNA Nano chip is very similar to running a DNA chip on the Bioanalyzer. However there are some things to keep in mind:

1. Clean everything with RNAse Away! before you start. I clean the chip loading stand as well as everything I am working with.

2. Make sure the reagents are at room temperature before you start to make the gel.

3. Before loading the chip, pipette 1.2 uL of each sample as well as the ladder into PCR tubes and incubate in the thermocycler for 2 minutes.

On the last point, I aliquot my samples into the PCR tubes and incubate them right before I load the gel. The instructions say to denature all the ladder in one go, but I have had better results when I denature an aliquot with my samples right before I run the chip.

Attached is a chip of 12 conifer leaf tissue extractions that worked out pretty well.

Conifer RNA Chip