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protocol_template_sampling.md

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methodology_category sample collection
project
purpose biodiversity assessment objective [OBI:0001969]
analyses filtration [OBI:0302885], environmental material collection process [OBI:0600012]
geographic_location
broad_scale_environmental_context
local_environmental_context
environmental_medium
target deoxyribonucleic acid (DNA) [NCIT:C449]
creator
materials_required filtration [OBI:0302885]
skills_required sterile technique, pipetting skills, standard molecular technique, research vessel experience
time_required
personnel_required 1
language en
issued
audience scientists
publisher
hasVersion 1
license CC0 1.0 Universal
maturity level mature
samp_category
env_broad_scale
env_local_scale
env_medium
habitat_natural_artificial_0_1
samp_collect_method
samp_collect_device
samp_size
samp_size_unit
samp_store_temp
samp_store_sol
samp_mat_process
filter_passive_active_0_1
prefilter_material
size_frac_low
size_frac
filter_diameter
filter_material

Protocol Template -- Sampling

PROTOCOL INFORMATION

Minimum Information about an Omics Protocol (MIOP)

  • MIOP terms are listed in the YAML frontmatter of this page.
  • See MIOP_definition.md for list and definitions.

Making eDNA FAIR (FAIRe)

Authors

  • All authors known to have contributed to the preparation of this protocol, including those who filled in the template.
  • Visit https://orcid.org/ to register for an ORCID.
  • Date is the date the author first worked on the protocol.
PREPARED BY AFFILIATION ORCID DATE
Content Cell Content Cell Content Cell yyyy-mm-dd
Content Cell Content Cell Content Cell yyyy-mm-dd

Related Protocols

  • This section contains protocols that should be known to users of this protocol.
  • Include the link to each protocol.
  • Include the version number and release date (if available).
  • Internal/External: "Internal" are derivative or altered protocols, or other protocols in this workflow. "External" are protcols from manufacturers or other groups.
PROTOCOL NAME LINK VERSION RELEASE DATE INTERNAL/EXTERNAL
Content Cell Content Cell Content Cell yyyy-mm-dd Content Cell
Content Cell Content Cell Content Cell yyyy-mm-dd Content Cell

Protocol Revision Record

  • Version numbers start at 1.0.0 when the protocol is first completed and will increase when changes that impact the outcome of the procedure are made (patches: 1.0.1; minor changes: 1.1.0; major changes: 2.0.0).
  • Release date is the date when a given protocol version was finalised.
  • Description of revisions includes a brief description of what was changed relative to the previous version.
VERSION RELEASE DATE DESCRIPTION OF REVISIONS
1.0.0 yyyy-mm-dd Initial release

Acronyms and Abbreviations

ACRONYM / ABBREVIATION DEFINITION
Content Cell Content Cell
Content Cell Content Cell

Glossary

SPECIALISED TERM DEFINITION
Content Cell Content Cell
Content Cell Content Cell

BACKGROUND

This document describes the required protocol to conduct [insert name of the method/protocol].

Summary

Insert a short description of the background for the method/protocol (e.g. why and for which purpose do you perform water sampling). Please provide a brief summary of your method including, as appropriate, a brief description of what techniques your best practice is about, which ocean environments or regions it targets, the primary sensors covered, what type of data/measurements/observing platform it covers, limits to its applicability.

Method Description and Rationale

Insert a short description of the functioning principal of the methodology used in the protocol (i.e. how does the method work?). Please note that this is different from the step-by-step description of the protocol procedure. Insert a short statement explaining why the specific methodology used in the protocol has been selected (e.g. it is highly reproducible, highly accurate, procedures are easy to execute etc….).

Spatial Coverage and Environment(s) of Relevance

If applicable, please specify the region where the protocol is applied. For regional term guidance see the GAZ ontology. If applicable, please indicate here the environment(s) of relevance for the protocol, e.g. Abyssal plain. Select from the ENVO ontology.

PERSONNEL REQUIRED

Insert the number of technicians, data managers, and scientists required for the good execution of the procedure

Safety

Identify hazards associated with the procedure and specify protective equipment and safety training required to safely execute the procedure

Training Requirements

Specify technical training required for the good execution of the procedure.

Time Needed to Execute the Procedure

Specify how much time is necessary to execute the procedure.

EQUIPMENT

  • Description: E.g., "filter".
  • Product Name and Model: Provide the official name of the product.
  • Manufacturer: Provide the name of the manufacturer of the product.
  • Quantity: Provide quantities necessary for one application of the standard operating procedure (e.g., number of filters).
  • Remark: For example, some of the consumable may need to be sterilized, some commercial solution may need to be diluted or shielded from light during the operating procedure.
DESCRIPTION PRODUCT NAME AND MODEL MANUFACTURER QUANTITY REMARK
Durable equipment
Content Cell Content Cell Content Cell Content Cell Content Cell
Content Cell Content Cell Content Cell Content Cell Content Cell
Consumable equipment
Content Cell Content Cell Content Cell Content Cell Content Cell
Content Cell Content Cell Content Cell Content Cell Content Cell
Chemicals
Content Cell Content Cell Content Cell Content Cell Content Cell
Content Cell Content Cell Content Cell Content Cell Content Cell

STANDARD OPERATING PROCEDURE

In the following SOP, please use the exact names of equipment as noted in the table above.

Provide a step-by-step description of the protocol. The identification of difficult steps in the protocol and the provision of recommendations for the execution of those steps are encouraged.

Preparation

Please specify the preparatory actions you took before you collected the samples and note what equipment was needed to do so (e.g. disinfection of work surfaces, preparations to the equipment you intend to use later on).

  1. [Step 1]
  2. [Step 2]

Sampling

Please specify how you collected samples and note what equipment you used to do so (e.g. targeted water mass, volume, sampling equipment, replication).

  1. [Step 1]
  2. [Step 2]

Filtration

Please specify how you filtered the samples and note what equipment you used to do so (e.g. mixing, volume filtered, size of filter and pores, filtration apparatus, duration of filtration, replication).

  1. [Step 1]
  2. [Step 2]

Sample Preservation

Please specify what steps you took to preserve the samples taken and note what equipment you used to do so (e.g. freezing in liquid nitrogen).

  1. [Step 1]
  2. [Step 2]

Storage

Please specify how you stored your samples and note what equipment you used to do so (e.g. stored in -80°C freezer).

  1. [Step 1]
  2. [Step 2]

Quality Control

Describe and explain criteria used to validate results of the standard operating procedure.

Basic Troubleshooting Guide

  • Identify known issues associated with the procedure, if any.
  • Provide troubleshooting guidelines when available.

REFERENCES

APPENDIX A: DATASHEETS

Link templates (e.g. preformatted spreadsheets) used to record measurements and report on the quality of the data as well as any documents such as manufacturer specifications, images, etc that support this protocol. Please include a short note describing the document's relevance.