MIOP Term | Value | |
analyses | DNA extraction [OBI:0000257] | |
audience | scientists | |
broad-scale environmental context | marine biome ENVO_00000447 | |
creator | Jacoby Baker, https://orcid.org/0000-0002-0673-7535 | |
environmental medium | sea water [ENVO:00002149] | filter paper [OBI:0000151] | |
geographic location | Monterey Bay [GAZ:00002509] | |
hasVersion | 3 | |
issued | 2023-11-07 | |
language | en | |
license | CC BY 4.0 | |
local environmental context | oceanic epipelagic zone biome [ENVO:01000033] | |
materials required | centrifuge [OBI:0400106] | incubator [OBI:0000136]] | |
maturity level | Mature | |
methodology category | sample extraction and purification | |
personnel required | 1 | |
project | Marine Biodiversity Observation Network (MBON) | |
publisher | Monterey Bay Aquarium Research Institute, Chavez Lab | |
purpose | DNA extraction [OBI:0000257] | |
skills required | sterile technique | pipetting skills | |
target | DNA | |
time required | 1320 |
PREPARED BY All authors known to have contributed to the preparation of this protocol, including those who filled in the template. | AFFILIATION | ORCID (visit https://orcid.org/ to register) | DATE | |
Jacoby Baker | MBARI | 0000-0002-0673-7535 | 2023-11-07 | |
N. Kobun Truelove | MBARI | 0000-0002-2236-1849 | 2023-11-07 | |
Kathleen J. Pitz | MBARI | 0000-0002-4931-8592 | 2023-11-07 |
PROTOCOL NAME AND LINK | ISSUER / AUTHOR | RELEASE / ACCESS DATE | |
Qiagen DNeasy 96 Blood and Tissue Kit Protocol | Qiagen | 2023-11-7 | |
https://mbari-bog.github.io/MBON-Protocols/eDNA_extraction_V3.html | Jacoby Baker | 2023-11-07 |
ACRONYM / ABBREVIATION | DEFINITION | |
PVDF | polyvinylidene difluoride | |
GFF | Glass Microfiber Filters | |
art. comm | Artificial Community | |
eDNA | environmental DNA |
SPECIALISED TERM | DEFINITION | |
Content Cell | Content Cell | |
Content Cell | Content Cell |
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. | |
Durable equipment | |||||
incubator | Gyromax 702 | Amerex instruments | |||
centrifuge | Sorvall Legend XTR centrifuge | Thermo scientific | CAT# 75004521 | ||
bead beater | TissueLyser II | Qiagen | CAT# 85300 | ||
Consumables | |||||
Qiagen DNeasy 96 Blood & Tissue Kit | Qiagen DNeasy 96 Blood & Tissue Kit | Qiagen | |||
Chemicals | |||||
ethanol (96–100%) | |||||
RNase Away | RNase Displace | FoxWest sales | CAT# 1401 | ||
EtOH wash | 70% ethanol | ||||
NF H2O | Nuclease-Free water | Invitrogen | CAT# AM9932 |