Aug 01, 2023

Public workspaceEnvironmental DNA (eDNA) Sample Shipping Protocol

DOI
https://dx.doi.org/10.17504/protocols.io.dm6gp38jpvzp/v1
Environmental DNA (eDNA) Sample Shipping Protocol
  • Meghan M. Shea1,
  • Alexandria Boehm1
  • 1Stanford University
Meghan M. Shea
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DOI: https://dx.doi.org/10.17504/protocols.io.dm6gp38jpvzp/v1
Protocol Citation: Meghan M. Shea, Alexandria Boehm 2023. Environmental DNA (eDNA) Sample Shipping Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dm6gp38jpvzp/v1
Manuscript citation:
Shea, M. M., & Boehm, A. B. (2024). Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal. Environmental DNA, 6(2), e521. https://doi.org/10.1002/edn3.521
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: June 19, 2023
Last Modified: August 01, 2023
Protocol Integer ID: 83661
Keywords: PCR amplicons, eDNA, shipping, environmental DNA, environmental dna, sample shipping protocol, dna, georgia genomic, edna sample, mailing pcr amplicon, pcr protocol, successful shipping protocol, guidance on successful shipping protocol, bioinformatics core, pcr, protocol, relevant to other shipping context, pcr amplicon, other shipping context, edna
Abstract
This is a protocol for mailing PCR amplicons generated from eDNA samples, specifically via the following earlier sampling & filtration, extraction, and PCR protocols, e.g.:
Protocol
Coastal Environmental DNA Sampling & Gravity Filtration Protocol
NAME
Coastal Environmental DNA Sampling & Gravity Filtration Protocol
CREATED BY
Meghan M. Shea

Protocol
DNA Extraction Protocol from Sterivex Filters
NAME
DNA Extraction Protocol from Sterivex Filters
CREATED BY
Meghan M. Shea

Protocol
Environmental DNA (eDNA) COI PCR Amplification and Gel Electrophoresis Protocol
NAME
Environmental DNA (eDNA) COI PCR Amplification and Gel Electrophoresis Protocol
CREATED BY
Meghan M. Shea
While this protocol was designed for mailing to the Georgia Genomics and Bioinformatics Core, the general principles may be relevant to other shipping contexts.


Acknowledgements & Attributions:

Thanks to Bradley B. Tolar for guidance on successful shipping protocols.
Image Attribution
Meghan M. Shea
Materials
General Laboratory Equipment:


EquipmentSpecific Model Used
10% bleach solution in spray bottleNA
>70% ethanol solution in spray bottleNA
RNase Away solution in spray bottleNA
20 µL multichannel pipette with sterile tipsVarious
UV CrosslinkerUVP CL-1000 Ultraviolet Crosslinker
PCR Tube HoldersVarious
Ice binVarious
ParafilmVarious
KimwipesVarious
Shipping Supplies:

MaterialAmount NeededSourceLinkApprox. Cost
96-well plate1/96 samplesApplied Biosystems via ThermoFisher Scientific (4346906)https://www.thermofisher.com/order/catalog/product/4346906$129/20 plates
Aluminum adhesive seal for 96-well plate1/plateUnknownNAUnknown
CardboardEnough to cover both sides of each plateVariousNAUnknown
Ziploc bagsVariousVariousNAUnknown
Bubble wrapVariousVariousNAUnknown
Hard container for holding platesVariousVariousNAUnknown
Styrofoam cooler with associated outer cardboard box1Reagents previously shipped on iceNARecycled



Troubleshooting
Preparing Samples for Shipping
Clean bench area with 10% bleach, 70% ethanol, and RNase Away
Note
Ideally, this should be a designated post-PCR bench area.

Wipe down 20 µL multichannel pipette and several PCR tube holders with RNase away. Run in UV Crosslinker for 10 minutes on each side.
Wipe down ice bin with 10% bleach, 70% ethanol, and RNase Away, fill with ice, and add PCR products stored in 8-strip PCR tubes
Label all 96-well plates needed for storing samples accordingly
Being careful not to open PCR tubes directly over the 96-well plates, add 15 µL of sample to each well using multichannel pipette, making sure you keep track of the orientation of how the plate was filled
Seal the plates carefully with aluminum adhesive seals
Press around the edges of each well to make sure they are sealed
Parafilm around the edges of each plate
Wrap each plate in Kimwipes to absorb any condensation that occurs during shipping
Cut two pieces of cardboard that fit on either side of each plate; tape the cardboard around each plate to form a sandwich (to keep it from getting punctured while shipping)
Seal each plate in a new Ziploc bag and label accordingly
Bubble wrap around each plate and place in a hard container (cardboard freezer box, pipette tip box, etc.)
Seal hard container with tape and place in its own Ziploc bag; label accordingly
Place bagged box in a Styrofoam cooler that fits in an associated cardboard box and fill with ice packs
Tape Styrofoam cooler closed and secure it in the corresponding cardboard box
Note
If you need to include any order information or documents alongside the samples, don't forget to put them in the box here.

Store cardboard box at -20°C until ready to mail