Home page for NOAA 'Omics Github repository

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

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.

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.

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

This PCR protocol is for amplifying the mitochondrial displacement loop (D-loop) gene also known as the mitochondial control region in marine mammals.

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

Protocol for sampling water using Sterivex with no ZR beads or preservative (dry)

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

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.

This document describes the required protocol to conduct a Quantitative Polymerase Chain Reaction (qPCR) assay to detect and quantify double-stranded DNA of the NADH dehydrogenase 5 (nad5) gene from the sunflower star (Pycnopodia helianthoides) with an Internal Positive Control (IPC).

Protocol for extracting DNA from sediment trap samples using the Qiagen PowerSoil Pro Kit

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

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

This PCR protocol is for amplifying the 16S rRNA v4-v5 region.

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 12S V5-V6 (MiFish) amplicon libraries using MBARI protocol modified for SEAMAP