| Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp. from Narragansett Bay and the Northeast U.S. Shelf from 2018-2023 | Benchtop instrument. The LightCycler® 480 System features a versatile, plate-based, real-time PCR device that supports mono- or multicolor applications.
Roche, Pleasanton, CA, USA
| LightCycler480 |
| Symbiont titers in Bugula neritina colonies grown under different conditions | | Applied Biosystems StepOne Plus Real-Time PCR System |
| Cell-growth gene expression reveals a direct fitness cost of grazer-induced toxin production in red tide dinoflagellate prey | The system can be setup in a variety of configurations and comes ready to use, out of the box, with intuitive data analysis and instrument control software. Utilizing robust LED based 4-color optical recording, the StepOnePlus™ Real-Time PCR System is designed to deliver precise, quantitative Real-Time PCR results for a variety of genomic research applications.
| StepOnePlus™ real-time PCR system (Applied BiosystemsTM) |
| Microbial ESV counts for Acropora millepora corals exposed to Galaxaura seaweed | | |
| Microbial ESV counts for Acropora millepora corals exposed to Sargassum seaweed | | |
| Dissolved Organic Nitrogen oxidation collected on cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017 | All reactions (25 μL total volume) were run in triplicate on a C1000 Touch Thermal Cycler equipped with a CFX96 Real-Time System (Bio- Rad), using either the iTaq Universal Green SYBR Mix (Bio-Rad) or the Platinum qPCR SuperMix-UDG (Thermo Fisher).
| C1000 Touch Thermal Cycler |
| Population changes in Halobacteriovorax cultured with protist & prey | CFX96 Touch Deep Well Real-Time PCR Detection System (Bio-Rad, Hercules, CA 94547, USA)
| CFX96 Touch Deep Well Real-Time PCR Detection System |
| Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011. | BioRad CFX96 quantitative PCR machine (Bio-Rad, Inc. in Hercules, CA)
| BioRad CFX96 quantitative PCR machine |
| Proportions of healthy, pale, bleached, and dead Orbicella faveolata recruits over time during a heat stress laboratory experiment conducted in 2018 and 2019, corresponding to proportions of different symbiont genera hosted | For qPCR data, assays targeting specific actin loci for each genus were performed using a QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA).
| QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA) |
| Initial field conditions at Kane‘ohe Bay, Oahu, Hawaii and abundances of Parvocalanus crassirostris and Bestilina similis nauplii, May/June 2013 (EAGER: Copepod nauplii project) | | Roche LC96 thermalcycler |
| Size of B. neritina colonies with and without symbiont grown at different temperatures | | quantitative PCR |
| Quantitative PCR cell count estimates from samples of DNA extracted from seagrass wasting disease parasite, Labyrinthula zosterae from wasting disease mesocosm experiments at Bodega Marine Laboratory in July-Sept of 2015 | The focal leaf was stored for subsequent DNA extraction and quantitative PCR to estimate Labyrinthula zosterae cells as a proxy for infection. Software: Bio-Rad CFX Manager Software (version 3.1)
| Bio-Rad CFX96 Real-Time System |
| Seagrass metrics from from seagrass wasting disease mesocosm experiments conducted at Bodega Marine Laboratory from July-September 2015 | The focal leaf was stored for subsequent DNA extraction and quantitative PCR to estimate Labyrinthula zosterae cells as a proxy for infection. Software: Bio-Rad CFX Manager Software (version 3.1)
| Bio-Rad CFX96 Real-Time System |
| Microbial alpha diversity of Acropora millepora samples from a coral-seaweed competition experiment in the Fiji Islands, Dec. 2014 | | |
| 16S rRNA gene datasets, metagenomes, and metatranscriptomes from cores collected on R/V Knorr cruise KN223 in the North and West Atlantic Ocean from October to December 2014 | | |
| Prevalence and intensity of oyster parasite species following a reef restoration experiment in Quonochontaug Pond, Rhode Island, USA from 2017-2020 | Bio-Rad CFX96TM Real-Time System – used for qPCR analysis of oyster microparasites
| Bio-Rad CFX96 |
| Results of qPCR assessments of the abundance of genes related to nitrification, and measurements of ammonia, urea, nitrite and polyamine concentrations in samples collected on cruise LMG1801 on R/V Laurence M. Gould from January to February 2018 | | iCycler CFX Connect Real-Time PCR Detection System (BioRad) |
| Results from qPCR assays to quantify the abundance and photochemical performance of symbionts relative to coral cells in three coral species collected from colonies in southeast Florida in April and October 2019 before, during, and after heat stress tests | qPCR was performed using a QuantStudio3 real-time PCR system (Applied Biosystems).
| QuantStudio3 real-time PCR system |
| Limits of detection and qPCR efficiencies from cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017 | All reactions (25 μL total volume) were run in triplicate on a C1000 Touch Thermal Cycler equipped with a CFX96 Real-Time System (Bio- Rad), using either the iTaq Universal Green SYBR Mix (Bio-Rad) or the Platinum qPCR SuperMix-UDG (Thermo Fisher).
| C1000 Touch Thermal Cycler |
| Data resulting from testing dilution experiments conducted in the development of four assays to quantify copeod naupliar biomass in Kaneohe Bay, Hawaii | A light Cycler 96 Quantitative PCR Thermalcycler (Roche) was used for qPCR measurements.
| Light Cycler 96 Quantitative PCR Thermalcycler (Roche) |
| Measurements of mixed field samples used for qPCR estimates and estimating biomass of DNA copy number in bulk samples | A light Cycler 96 Quantitative PCR Thermalcycler (Roche) was used for qPCR measurements.
| Light Cycler 96 Quantitative PCR Thermalcycler (Roche) |
| Measurements of individual body size and qPCR estimates of DNA copy number per individual from the development of four assays to quantify copeod naupliar biomass in Kaneohe Bay, Hawaii | A light Cycler 96 Quantitative PCR Thermalcycler (Roche) was used for qPCR measurements.
| Light Cycler 96 Quantitative PCR Thermalcycler (Roche) |
| Area of Orbicella faveolata recruits hosting different proportions of various symbiont genera from a symbiont acquisition laboratory experiment conducted in 2018 and 2019 | For qPCR data, assays targeting specific actin loci for each genus were performed using a QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA).
| QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA) |
| qPCR data for Orbicella faveolata recruits throughout a symbiont acquisition laboratory experiment conducted in 2018 and 2019 | For qPCR data, assays targeting specific actin loci for each genus were performed using a QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA).
| QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA) |
| Survivorship and proportion of recruits infected with Symbiodiniaceae over time during a symbiont acquisition laboratory experiment conducted in 2018 and 2019 | For qPCR data, assays targeting specific actin loci for each genus were performed using a QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA).
| QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA) |
| Gene copy number counts and 16S analyses of July 2019 Rhode River surface water incubated with or without viral dilution | | CFX96 Real-Time PCR Detection System |
| Water quality data, gene copy number counts, and 16S analyses from Rhode River samples collected at SERC during 2017 and 2018 | | CFX96 Real-Time PCR Detection System |
| Spatiotemporal characterization of nirK and nirS abundance from R/V Polaris monthly San Francisco Bay USGS Water Quality cruises from July of 2011 to June of 2012 (N-Cycling Microbial Communities project) | StepOnePlus Real-Time PCR system (Applied Biosystems, Foster City, CA)
| StepOnePlus Real-Time PCR system |
| Symbiont community structure in Orbicella faveolata from Mermaid Reef and Sandy Cay Reef in Abaco, The Bahamas in January 2019 | | |
©2020 Biological and Chemical Oceanography Data Management Office.