Main repository for NOAA Pacific Marine Environmental Laboratory Ocean Molecular Ecology group bioinformatics and data analysis.

Collection of biomolecular protocol templates for an organization

Minimum Information about an Omics Protocol (MIOP) specifications

Water collection and filtration protocol using sterivex filters to collect environmental DNA from marine ecosystems. This collection and filtration protocol is used by the NOAA PMEL Ocean Molecular Ecology (OME) Group.

Protocols used by AOML Omics labs, following the BeBOP-OBON standard

Protocols for sampling, processing, and analysis of eDNA collected on CalCOFI cruises. All protocols are formatted according to guidelines from Better Biomolecular Ocean Practices (BeBOP) using Minimum Information about an Omics Protocol (MIOP) terms.

In lab and out of lab protocols for MBON eDNA collection and processing

This qPCR protocol is for amplifying and quantifying the nad2 gene in Dungeness crab (Metacarcinus magister).

Nucleic acids extraction from the sterivex filters using the Qiagen DNeasy Blood and Tissue Kit with some modifications to the manufacturer’s protocol. These extraction protocols, adapted from Spens et al 2017, are used by the NOAA PMEL Ocean Molecular Ecology (OME) Group.

Nucleic acids extraction from 47 mm disc filters using the Qiagen DNeasy Blood and Tissue Kit with some modifications to the manufacturer’s protocol. These extraction protocols, adapted from Spens et al 2017, are used by the NOAA PMEL Ocean Molecular Ecology (OME) Group.

Protocol for preparing 18S V9 (EMP) amplicon libraries for Michigan State RTSF

This PCR protocol is for amplifying This protocol is for amplifying the small subunit ribosomal ribonucleic acid (SSU rRNA) 18S v8 gene in eukaryotes.

This PCR protocol is for amplifying the Small subunit ribosomal ribonucleic acid (SSU rRNA) 18S v9 gene in eukaryotes.

This protocol is for running and imaging PCR product using gel electrophoresis.

This protocol is for quantifying the concentration of DNA in the product of a DNA extraction.

Protocol for preparing COI (Leray-Geller) amplicon libraries at Smithsonian NMNH

Water collection + EtOH subsampling protocol, plus subsequent filtration using disc filters and a vacuum manifold. This collection and filtration protocol is used by the NOAA PMEL Ocean Molecular Ecology (OME) Group.

Water collection and filtration protocol using sterivex filters and gravity bags to collect environmental DNA from marine ecosystems. This collection and filtration protocol is used by the NOAA PMEL Ocean Molecular Ecology (OME) Group.

This document describes the required protocol to conduct a Droplet Digital Polymerase Chain Reaction (ddPCR) assay to detect and quantify double-stranded DNA of the NADH dehydrogenase 5 (nad5) gene from the sunflower star (Pycnopodia helianthoides).