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[AT50-24 Bacterial 16S barcodes] - Bacterial 16S rRNA barcodes associated with methane seep invertebrates collected off of the Aleutian Islands, Gulf of Alaska on R/V Atlantis cruise AT50-24 from May to June 2024 (Collaborative Research: Redefining the footprint of deep ocean methane seepage for benthic ecosystems)

Listed in Biological and Chemical Oceanography Data Management Office (BCO-DMO) ERDDAP

Seep invertebrates were collected from the Sanak seep off of Alaska in June 2024 (53.74865 N/ −162.58970 W; 2,020 m) aboard the R/V Atlantis (expedition AT50-24) with HOV Alvin (operated by the Woods Hole Oceanographic Institution).

Description

Specimens for molecular analysis were preserved within 2 h of collection in ~90% ethanol and stored at 4 °C. Total genomic DNA was extracted from whole specimens preserved in ethanol using the Qiagen DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

Total DNA extracted was quantified via a Qubit 3.0 fluorometer using the dsDNA BR Assay Kit (Thermo Fisher Scientific). The V4-V5 hypervariable region of the 16S rRNA gene was PCR amplified using bacterial primers [515F: GTGYCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT] with Illumina adapters on the 5′ end (San Diego, CA). Each PCR product was secondarily barcoded with Illumina NexteraXT index v2 Primers that included unique 8-bp barcodes, with NEB Q5 Hot Start High-Fidelity Mix at an annealing temperature of 66 °C for 11 cycles.

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Barcoded products were purified using Millipore-Sigma (St. Louis, MO) MultiScreen Plate MSNU03010 with a vacuum manifold and quantified using the QuantIT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific) on a BioRad CFX96 Touch Real-Time PCR Detection System. Barcoded samples were combined in approximately equimolar amounts, purified again with Promega's Wizard SV Gel and PCR Clean-up System (#A9281), and quantified again using the QuBit system.

This sample was submitted to Laragen, Inc. (Culver City, CA) for 2× 250 bp paired-end analysis on the Illumina MiSeq platform with 20% PhiX addition.

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Provenance · 1 source records, 4 field assertions
SourceKeyLast seenRaw
Biological and Chemical Oceanography Data Management Office (BCO-DMO) ERDDAPbcodmo_dataset_1007825_v113 d agoJSON v1
FieldAssertionExtractorEvidence
access_levelsource · erddap bco dmo orgconnector:erddap_bco_dmo_org@1.0.0
concepts[field].local:field:ocean-atmosphericmapping · erddap bco dmo orgconnector:erddap_bco_dmo_org@1.0.0
descriptionsource · erddap bco dmo orgconnector:erddap_bco_dmo_org@1.0.0/summary
titlesource · erddap bco dmo orgconnector:erddap_bco_dmo_org@1.0.0/title