Jun 01, 2024

Public workspaceSerapure Beads Preparation and Testing

DOI
dx.doi.org/10.17504/protocols.io.3byl49952go5/v1
Serapure Beads Preparation and Testing
  • 1Hakai Institute
Andreas Novotny
Open access
DOI: dx.doi.org/10.17504/protocols.io.3byl49952go5/v1
External link: http://hakai.org
Protocol Citation: rute.carvalho Carvalho, Colleen Kellogg, Matt Lemay 2024. Serapure Beads Preparation and Testing. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl49952go5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: May 31, 2024
Last Modified: June 01, 2024
Protocol Integer ID: 101041
Abstract
This protocol is used to prepare low-cost SPRI beads used for Illumina Library preparations. As part of the Hakai Institute Ocean Observing Program, from 0 m to near bottom (260 m), biomolecular samples have been collected weekly to genetically characterize plankton communities in the Northern Salish Sea since 2015. These SPRI beads have been used to clean up PCR products of 16S, 18S, COI, and 12S amplicons, and implemented as part of a standard procedure for eDNA analysis.

This protocol is a modification from the following protocol:
B. Faircloth and T. Glenn. Serapure v2.2. Ecol. and Evol. Biology, UCLA, November 19, 2011
Which was based on the following article:
CITATION
Rohland N, Reich D. (2012). Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture.. Genome Res. 2012.
LINK
https://doi.org/10.1101/gr.128124.111

Protocol materials
Reagent6-Tube Magnetic Separation RackNew England BiolabsCatalog #S1506S
Step 1
ReagentUltraPure™ 1M Tris-HCI pH 8.0Thermo Fisher ScientificCatalog #15568025
In 3 steps
ReagentEDTA (0.5 M), pH 8.0Life TechnologiesCatalog #AM9260G
In 3 steps
ReagentSera-Mag SpeedBeads Carboxylate-Modified Magnetic ParticlesGE HealthcareCatalog #44152105050350
In 2 steps
ReagentPEG-8000 PromegaCatalog #V3011
In 2 steps
ReagentNaCl (5 M), RNase-freeThermo FisherCatalog #AM9759
In 2 steps
ReagentTWEEN 20 for molecular biology viscous liquidMerck MilliporeSigma (Sigma-Aldrich)Catalog #P9416-50ML
In 2 steps
ReagentGeneRuler 100 bp DNA Ladder Thermo Fisher ScientificCatalog #SM0241
Step 1
PREPARATIONS
PREPARATIONS
Materials (or equivalent):
ReagentSera-Mag SpeedBeads Carboxylate-Modified Magnetic ParticlesGE HealthcareCatalog #44152105050350
ReagentPEG-8000 PromegaCatalog #V3011
ReagentUltraPure™ 1M Tris-HCI pH 8.0Thermo Fisher ScientificCatalog #15568025
ReagentEDTA (0.5 M), pH 8.0Life TechnologiesCatalog #AM9260G
ReagentTWEEN 20 for molecular biology viscous liquidMerck MilliporeSigma (Sigma-Aldrich)Catalog #P9416-50ML
ReagentNaCl (5 M), RNase-freeThermo FisherCatalog #AM9759
ReagentGeneRuler 100 bp DNA Ladder Thermo Fisher ScientificCatalog #SM0241
Reagent6-Tube Magnetic Separation RackNew England BiolabsCatalog #S1506S

STEPS
STEPS
In a 50 mL conical using sterile stock solutions, prepare TE (10 mM Tris-HCl, 1 mM EDTA) by adding:
  • 500 µL ReagentUltraPure™ 1M Tris-HCI pH 8.0Thermo Fisher ScientificCatalog #15568025
  • 100 µL ReagentEDTA (0.5 M), pH 8.0Life TechnologiesCatalog #AM9260G
  • Fill conical to 50 mL mark with dH20.

Mix the container of ReagentSera-Mag SpeedBeads Carboxylate-Modified Magnetic ParticlesGE HealthcareCatalog #44152105050350 and transfer 1 mL to a 1.5 mL microtube.

Place SpeedBeads on amagnet stand until beads are drawn to magnet.
Remove supernatant with P200 or P1000 pipetter.
Add 1 mL TE to beads, remove from the magnet, mix, and return to the magnet.

Remove supernatant with P200 or P1000 pipetter.
Add 1 mL TE to beads, remove from the magnet, mix, and return to the magnet.

Remove supernatant with P200 or P1000 pipetter.
Add 1 mL TE to beads and remove from magnet. Fully resuspend and set microtube in the rack (i.e. not on magnet stand).

Add 9 g ReagentPEG-8000 PromegaCatalog #V3011 to a new 50 mL, sterile conical.

Add 10 mL ReagentNaCl (5 M), RNase-freeThermo FisherCatalog #AM9759 (or 2.92 g NaCl) to conical.

Add ReagentUltraPure™ 1M Tris-HCI pH 8.0Thermo Fisher ScientificCatalog #15568025 to conical.

Add 100 uL ReagentEDTA (0.5 M), pH 8.0Life TechnologiesCatalog #AM9260G to conical.

Fill conical to ~ 49 mL using sterile dH20. You can do this by eye, just go slowly.
Mix conical for about 3-5 minutes until PEG goes into solution (solution, upon sitting, should be clear).
Add 27.5 µL ReagentTWEEN 20 for molecular biology viscous liquidMerck MilliporeSigma (Sigma-Aldrich)Catalog #P9416-50ML to conical and mix gently.

Mix the 1mL SpeedBead + TE solution and transfer to 50 mL conical.

Fill conical to 50 mL mark with dH20 (if not already there) and gently mix 50 mL conical until brown.
Test against AMPure XP using aliquots of ladder (Fermentas GeneRuler). I recommend the 50 bp ladder in place of the ultraNlow range ladder.
Wrap in tinfoil (or place in dark container) and store at 4°C.


Note
You may also wish to prep an extra 50 mL of PEG solution that lacks Sera-mag SpeedBeads so that you can use it in a bead-inclusive library preparation protocol, derived from Fisher (2011).
In that case, just:
1. Add 10 g PEGN8000 to a new 50 mL, sterile conical.
2. Add 25 mL ReagentNaCl (5 M), RNase-freeThermo FisherCatalog #AM9759
(or 7.3 g NaCL) to conical.
3. Fill conical to ~ 49 mL using sterile dH20. You can do this by eye, just go slowly.
4. Mix conical for about 3-5 minutes until PEG goes into solution (solution, upon sitting,
should be clear).

Test monthly.
TESTING
TESTING

Note
You should test the Serapure mixture to ensure that it is working as expected. You can do this
using DNA ladder (Fermentas GeneRuler – NEB ladders may cause problems).

Prep fresh aliquots of 70% EtOH.

Mix 2 µL GeneRuler with 18 µL dH20.

Add 20 µL GeneRuler mixture to a volume of Serapure and/or AMPure (the specific volume depends on whether you are trying exclude small fragments or not; see the figure on the next page).

Incubate mixture for 5 min at room temperature.

Place on magnet stand.
Remove supernatant.
Add 500 µL 70% EtOH.

Incubate on stand for 1 min.

Remove supernatant.
Add 500 µL 70% EtOH.

Incubate on stand for 1 min.

Remove supernatant.
Place beads on 37°C heat block for 3-4 min. until dry.

Rehydrate with 20 µL dH20.

Place on magnet stand.
Transfer the supernatant to a new tube.
Mix supernatant with 1 µL loading dye.

Electrophorese in 1.5 % agarose for 1h at 100 V.

Citations
Rohland N, Reich D. . Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture.
https://doi.org/10.1101/gr.128124.111