Sample Collection, Preservation & Shipping for DNA Barcoding

Getting DNA barcoding steps right begins long before PCR. This guide explains how to collect, preserve, and ship specimens so sequences are clean, metadata are audit-ready, and downstream analysis moves quickly. You'll learn which media to use in the field, how to label with INSDC qualifiers, and how to package samples under UN3373 / IATA PI650 so they arrive without delays.

Essential pre-barcoding steps: collect and preserve specimens, apply INSDC-compliant labels, store correctly, and ship under UN3373/IATA PI650.

Field choices decide lab success

Most sequencing failures start in the field, not at the thermocycler. DNA begins degrading as soon as a specimen is collected. Rapid dehydration (silica gel), high-proof ethanol, or validated room-temperature buffers slow that process; poor choices (dilute alcohol, heat, formalin) accelerate it. Insects and plant tissues dried in silica often yield robust barcodes; soft tissues held in 95–100% ethanol perform well when the alcohol is kept in favorable proportion to the tissue and replenished when diluted.

Small habits also matter. Clean tools between samples, change gloves when switching matrices, and work on a clean surface. Record where and when each sample was collected using controlled vocabularies so your records load smoothly into BOLD Systems and GenBank.

Quick-start SOP: sampling essentials by material

Copy this section into your field manual. It focuses on simple, low-risk steps that protect DNA quality while keeping paperwork and logistics manageable.

Swabs & trace material

Use sterile, individually wrapped swabs; avoid touching non-target surfaces before sampling.
If cold chain is limited, place swabs into a validated room-temperature buffer (e.g., DESS or Longmire/NAP), then cap tightly. Otherwise, air-dry and store in a clean tube with a small desiccant sachet.

Head-to-head tests show EDTA-based DESS effectively preserves high-molecular-weight DNA at ambient temperature. (Sharpe A. (2020) PLOS ONE) Comparative tests show EDTA-containing DESS preserves high-molecular-weight DNA effectively at ambient temperature (Sharpe A. (2020) PLOS ONE).

Label tubes immediately and record site and matrix on the field sheet.

Animal tissues and fin clips

Sample size: a grain-of-rice is typically enough for Sanger barcoding.
Preserve in 95–100% ethanol; keep the sample:ethanol ratio generous to maintain concentration (a ~5:1 ethanol-to-sample volume is a common practical guideline).
Avoid formalin; cross-linking complicates DNA recovery. If a cold chain is available, freeze at −20 °C on return.

Insects and other arthropods

Place whole specimens in 95% ethanol or dry on silica gel; drain excess ethanol before shipping to reduce leakage risk.
For tiny specimens, pinning is acceptable if you also preserve a small tissue or leg in ethanol or silica for DNA extraction.

Plants and fungi

Collect small leaf punches, needles, or thin tissue strips; avoid thick, water-rich fragments.
Dry rapidly in fresh silica gel; replace or regenerate gel when an indicator changes color. Pressed vouchers plus silica-dried tissue deliver reliable results and simpler shipping.

Tip: Note the matrix (tissue type) on your form—muscle, fin, leaf, sporocarp—so the lab selects the appropriate extraction chemistry on receipt.

Drying protocol strongly impacts DNA integrity and yield, supporting rapid desiccation for downstream barcoding. (Forrest L.L. et al. (2019) Frontiers in Ecology & Evolution) Drying method markedly affects DNA integrity and yield, supporting rapid desiccation for downstream barcoding (Forrest L.L. et al. (2019) Frontiers in Ecology & Evolution).

Preservation media & decision tree

Choose media based on matrix, travel time, and regulations. The goal is to inhibit nucleases and microbial growth while keeping extraction straightforward.

95–100% ethanol

Pros: Inexpensive, widely validated, familiar to most labs.
Cons: Shipping restrictions; diluted by "wet" tissues; may need top-ups on long trips.
Use when: You can source high-proof ethanol and manage volumes legally.

Silica gel desiccation

Pros: No liquids; field-friendly; ideal for plants and small tissues; straightforward export.
Cons: Requires enough active gel and airtight containers; less ideal for large, water-rich tissues.
Use when: Liquid preservatives are impractical or restricted.

DESS / Longmire / NAP buffers

Pros: Preserve DNA at room temperature; components help inhibit nucleases and microbial growth; excellent for swabs and some soft tissues.
Cons: Buffer volumes may need to match or exceed sample mass; confirm compatibility with downstream protocols.
Use when: Cold chain is impossible and ethanol transport is restricted.

Cold chain (−20 °C / −80 °C)

Pros: Excellent for DNA integrity and fatty tissues.
Cons: Dry ice or liquid nitrogen logistics raise cost and complexity; airline restrictions apply.
Use when: You have reliable cold transport from field to lab.

Decision flow: If liquid transport is allowed, choose high-proof ethanol for tissues and whole arthropods. If not, use silica for plants or a room-temperature buffer for swabs/soft tissue. Where infrastructure allows, freezing is ideal.

Labeling, metadata & chain-of-custody

Good metadata turn samples into evidence. Capture fields that align with BOLD and INSDC so your records flow into databases without edits.

On the tube (waterproof label):

Sample ID (unique)
Medium (EtOH %, silica, DESS)
Collector initials

In the field log (paper or mobile app):

Specimen or voucher code (museum/herbarium, if applicable)
collection-date (use ISO-style formats recognized by INSDC)
geo_loc_name (controlled country/region strings)
Matrix (tissue type), site, permit, and storage conditions
Chain-of-custody entries: who handled the sample and when.

Preparing BOLD specimen records. Minimum fields to initiate a record include Sample ID, Field ID and/or Museum voucher ID, Institution storing the specimen, Phylum, and Country. Add trace files and sequences later.

Why this matters: Harmonized /geo_loc_name and /collection_date reduce submission errors and make sequences discoverable by region and time window.

Packaging & shipping compliance

Shipping biological samples safely and legally protects you and your carrier—and keeps packages moving.

When do UN3373 / IATA PI650 rules apply?

Many preserved specimens for barcoding are shipped as "Biological Substance, Category B" (UN3373) when they meet the scope; these shipments must follow PI650 triple-packaging requirements. Confirm classification with your institution's biosafety officer.

Triple packaging essentials (PI650):

Primary receptacle: Leak-proof tube or vial.
Secondary packaging: Leak-proof, pressure-tested container with sufficient absorbent material.
Outer packaging: Rigid, clearly labeled with the UN3373 diamond mark.

Include the responsible person name and phone number and, where applicable, show "UN3373 / Biological Substance, Category B" on the air waybill.

Ethanol considerations:

Carriers and jurisdictions limit volumes of flammable liquids. Drain excess ethanol where possible, or switch to silica/buffer alternatives before shipment. Confirm carrier-specific rules before you pack.

Compliance note: Shipping classifications and requirements vary by jurisdiction and carrier. Confirm details with your institutional biosafety officer and the latest IATA/WHO guidance. This article provides general information and is not legal advice.

On receipt at the lab:

Log package condition, reconcile Sample IDs against the field sheet, and capture any temperature logger data. This starts the lab's accession record and supports future audits.

Acceptance & rejection checklist

Use this drop-in SOP block to improve first-pass acceptance:

Tubes sealed; legible Sample ID matches the field sheet.
Medium declared (95% ethanol / silica / buffer / frozen) and volume sufficient.
Metadata present: collection-date (INSDC format), geo_loc_name (controlled vocabulary), matrix, collector, and permit (if required).
No formalin; no bleach; no broken or leaking containers; secondary containment intact.
Temperature logger present if cold chain used; chain-of-custody signed.
Receiving lab creates or updates BOLD specimen records with minimal fields, then proceeds to extraction.

FAQs

1) Is 70% ethanol okay for DNA barcoding?

Use 95–100% ethanol whenever possible. Lower concentrations allow more water and enzyme activity, increasing degradation risk. If high-proof ethanol is unavailable, switch to silica gel for plants or a validated room-temperature buffer (such as DESS/Longmire) for swabs or small tissues.

2) Can I ship swabs at room temperature?

Yes—if preserved in a validated buffer and packaged under UN3373 / PI650. Include absorbent material, use a rigid outer container, and follow carrier instructions. Confirm requirements with your carrier before shipping.

3) What minimum data do BOLD and GenBank expect?

BOLD requires a Sample ID, a field or museum voucher ID, institution, phylum, and country to open a record. GenBank/INSDC expect standardized qualifiers such as /collection_date and /geo_loc_name when you submit sequences.

4) How long can tissue stay in silica?

When silica gel is fresh and containers are airtight, plant tissues often remain stable for weeks to months at room temperature. Replace or regenerate silica as it saturates to maintain drying efficiency.

5) Is DESS better than ethanol?

Not universally. DESS and related buffers preserve DNA at room temperature and are useful when ethanol or cold chain is impractical. Ethanol remains simple and effective where permitted; choose based on matrix, regulations, and downstream needs.

6) When to switch to metabarcoding/eDNA?

If a sample likely contains DNA from many organisms—for example, water filters, soil, feces, or bulk invertebrate mixes—single-specimen barcoding becomes inefficient. Choose an eDNA/metabarcoding workflow designed for mixed templates, and plan collection around volume, filter pore size, preservation buffer, and inhibitor controls.

Action: start your project

Copy-paste SOP for the field kit

Pack sterile swabs, forceps, scissors or single-edge razors, spare waterproof labels, and gloves.
Choose media per matrix: 95–100% ethanol (with spare for top-ups), silica gel, or DESS/Longmire for swabs.
Pre-print IDs; bring a logbook or app to capture /collection_date and /geo_loc_name in controlled formats.
Carry secondary containers, absorbent material, and a rigid outer box to meet PI650.
On return, reconcile counts and start BOLD records with the minimal fields; attach images and add trace files later.

Related reading on our site:

References

Forrest, L.L., Hart, M.L., Hughes, M. et al. The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques. Frontiers in Ecology and Evolution 7, 439 (2019).
Sharpe, A., Barrios, S., Gayer, S. et al. DESS deconstructed: Is EDTA solely responsible for protection of high molecular weight DNA in this common tissue preservative? PLOS ONE 15(8), e0237356 (2020).
Ramón-Laca, A., Mourier, T., Gaughran, S.J. et al. A workflow for the relative quantification of multiple fish species from oceanic water samples using environmental DNA (eDNA) to support large-scale fishery surveys. PLOS ONE 16(9), e0257773 (2021).
Oakey, A., Grote, M., Smith, A. et al. Integrating drones into NHS patient diagnostic logistics systems: Flight or fantasy? PLOS ONE 17(12), e0264669 (2022).
Seutin, G., White, B.N., Boag, P.T. Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology 69(1), 82–90 (1991).

* Designed for biological research and industrial applications, not intended for individual clinical or medical purposes.