| 16S microbiome metadata collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021 | Thermal cycler - Used for polymerase chain reaction
| Thermal cycler |
| 16S rRNA gene amplicon sequence accessions collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project) | Bio-Rad C1000 Touch Thermocycler
| |
| 16S rRNA gene NCBI ID numbers from the PICO project | Used for PCR reactions
| Thermocyler |
| 16S rRNA sequence data from venting fluids and microbial mats; collected on R/V Atlantis cruise AT18-08 at the Axial Seamount, Juan de Fuca Ridge in 2011 | | |
| 16S V4 rRNA gene tag sequences from reef seawater samples collected in the Florida Keys and the U.S. Virgin Islands in 2019-2020 | | PCR |
| 515F-926R 16S rRNA gene sequencing accessions from seawater and sediment samples from R/V Falkor FK141109 and R/V Thompson TN309 from the Mariana and Kermadec trenches, 2014 (Mariana Perspectives project) | | |
| Field collection data for taxa detected in Copepod nauplii guts analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | | Thermal Cycler |
| Taxa detected in field caught nauplii guts analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | | Thermal Cycler |
| GenBank BLAST results of copepod nauplii gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | | Thermal Cycler |
| Identification of copepod gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | | Thermal Cycler |
| Accession numbers for genetic sequences of virus-enriched field samples and P. carterae viruses from laboratory cultures at Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016 | | Bio Rad icycler |
| Information about sequences of coral, Acropora cervicornis, collected from host colonies at the Mote Marine Laboratory in situ coral nursery in Looe Key, Lower Florida Keys in November and December 2019 | | PCR |
| Sequences from the coral Acropora cervicornis determined before and after bleaching at the Mote Marine Laboratory in August and September 2015 | | polymerase chain reaction (PCR) |
| Multilocus microsatellite genotypes of Acropora palmata from the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project) | | ABI 3730 |
| Mutations at microsatellite loci of Acropora palmata in the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project) | | ABI 3730 |
| Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp. from Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023 | | Eppendorf Mastercycler EP Thermal Cycler Series |
| Amplicon sequencing of ammonia oxidizing archaea amoA gene from R/V Kilo Moana KM1314 in the North Pacific Ocean, Aug-Sept 2013 (Nitrification and Planktonic Biodiversity project) | | |
| Overview of population samples included in genetic analyses of Pleuromamma xiphias (Plankton Population Genetics) | Polymerase Chain Reaction (PCR) amplification of a 681-bp fragment of mtCOI was conducted with primers and PCR and sequencing protocols as described in (Goetze, 2011).
| PCR |
| Sub-seafloor metatranscriptomes from anaerobic Peru Margin sediments collected on R/V JOIDES Resolution Leg 201 in 2002 | Absence of DNA and RNA contamination was confirmed by no visible amplification of small subunit (SSU) ribosomal RNA (rRNA) and rRNA genes from extraction blanks after 35 cycles of PCR and RT–PCR.
| PCR |
| Iberian Margin Anaerobic Sediment 18S rRNA amplicons from R/V JOIDES Resolution cruise JRES-339 in the West Iberian margin from 2011-2012 (Subseafloor Microbial Ecology project) | | |
| ARISA relative abundances (bacterial community structure), San Pedro Channel, 5 depths, 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project) | | Thermal Cycler |
| Assembled metagenome sequences collected on the R/V Melville (MGLN10MV) and R/V Atlantis (Alvin AT11-07) cruises in the Loihi Seamount, Hawaiian archipelago and East Pacific Rise from 2011-2013 (EPR and Loihi basalt genomes project) | DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA)
| |
| BLAST results from the Bermuda Atlantic Time Series (BATS) site collected from the R/V Atlantic Explorer cruises in Feb. and Aug. 2012 (DimBio NABE project) | Life Technologies AccuPrime PCR system
| |
| Sample log for 16S and 18S rDNA amplicons sequenced with 454 technology collected on the R/V Atlantic Explorer BATS site in 2012 (DimBio NABE project) | Life Technologies AccuPrime PCR system
| |
| Genotypes of symbionts in Muricea atlantica, M. elongata, and Plexaurella dichotoma across the 2015 Bleaching event (May 2015-August 2017) in the Florida Keys | DNA amplifications were performed on a BioRad T100 thermal cycler.
| BioRad T100 thermal cycler |
| Microsatellite loci for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C | Used to amplify microsatellite loci.
| a PTC-100 MJ Research Inc. thermal cycler or a BioRad T100-Thermal Cycler |
| Bugula neritina host genotype and symbiotic status of colonies along the East Coast, USA, ranging from latitudes 38.61283 to 29.753272 | | |
| Hemichordata and Echinodermata NCBI accessions, Table 2, Cannon et al (2013) Biol. Bull. (Antarctic Inverts project) | | |
| Hemichordata and Echinodermata GenBank accessions, Table S2, Cannon et al (2014) Curr. Bio. (Antarctic Inverts project) | | |
| Caribbean wide survey of PaV1 prevalence in adult lobsters in lobster fishing grounds from 2006-2007 and 2010-2011 (Lobster disease connectivity project) | | pCR |
| Sequence accession numbers for coral acid rich proteins (CARPs) from Stylophora pistillata; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) | Amplifications of the 16S and 18S rRNA were performed using a Perkin Elmer-Cetus 480 thermal cycler.
| Perkin Elmer-Cetus 480 thermal cycler |
| DNA sequences of viruses associated with copepods collected from the shoreside from Tampa Bay, Florida from 2004-2011 (Viruses in Copepods project) | DNA amplification was conducted using a Bio Rad Thermal Cycler (no model number available, for more information see http://www.bio-rad.com/en-us/category/thermal-cyclers). | Thermal Cycler |
| Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016 | | |
| cDNA expressed sequence tags for the corals Acropora palmate and Orbicella faveola in Mexico, Panama, and the Florida Keys in 2003 (SymBioSys project) | | |
| Accession numbers and images of coral samples taken in the Florida Keys during 2013 (Coral Microbial Relationships project) | Reactions carried out on a Bio-Rad thermocycler (Bio-Rad Laboratories, Inc., Hercules, CA, USA)
| Bio-Rad thermocycler |
| Illumina sequenced 16S rRNA genes amplified from the different life stages of 2 corals in Kaneohe Bay, Oahu, Hawaii during 2010 (MiCoDe project) | MyCycler thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA)
| Thermal Cycler |
| Hawaiian coral terminal-restriction fragment length polymorphism (T-RFLP) analysis collected from the R/V Hi'ialakai in Hawaiian Archipelago, Johnston Atoll, and American Samoa during 2005 (MiCoDe project) | MyCycler thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA)
| Thermal Cycler |
| Terminal restriction fragments from 16S rRNA genes amplified from coral-associated microbes in response to temperature stress from Kaneohe Bay, Oahu, Hawaii in 2007 (MiCoDe project) | MyCycler thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA)
| Thermal Cycler |
| Bacterioplankton data from coral and coral mucus aquaria experiments conducted at Bermuda Institute of Ocean Sciences in 2013 | Reactions carried out on a Bio-Rad thermocycler.
| Bio-Rad thermocycler |
| Specificity of associations between bacteria and Pocillopora meandrina during early development in Kaneohe Bay, Oahu, Hawaii from 2008 (MiCoDe project) | MyCycler thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA)
| Thermal Cycler |
| T-RFLP, response of the microbial community to coral spawning, lagoon and reef flats in Kaneohe Bay, Oahu, Hawaii during 2006 - 2007 (MiCoDe project) | MyCycler thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA)
| Thermal Cycler |
| Population genomics study on the planktonic pteropod Cuvierina spp.: RADSeq data and metadata (Plankton Population Genetics project) | | |
| GenBank accessions and links for DNA sequences for three genes (COI, 16S, H3) from Elysia cornigera and E. timida (Gastropoda: Sacoglossa)in Krug et al (2011) Invert. Syst.(PLDvFST project) | | |
| Accessions and links for DNA sequences for three genes (COI, 16S, H3) from 18 species in order Sacoglossa (Gastropoda) from Krug et al (2011) Invert. Syst. (PLDvFST project) | | |
| Philine spp. collection data and NCBI accessions links for 16S haplotype sequences from Krug et al (2012) Biol. Invasions (PLDvFST project) | | |
| GenBank accessions and links for sequences of three genes (COI, 16S, H3) for five Elysia spp., chiefly E. pusilla: Vendetti et al (2012) Integ. and Comp. Biol. (PLDvFST project) | | |
| Sequences of two genes (COI, H3) for three species complexes (Elysia abei, "Plakobranchus occelatus", Thuridilla carlsoni, Elysia atroviridis): Krug et al (2013) Molec. Phylogen. Evol. (PLDvFST project) | | |
| Molecular species delimitation and gene flow in Oxynoe (PLDvFST project) | | |
| Sub-seafloor sediment eukaryotic rRNA collected on R/V JOIDES Resolution Legs 201 and 204, R/V Maria Merian cruise MSM11-1 at North Pond, and R/V Meteor cruise M76-1a at the Benguela Upwelling System from 2002-2009 | | PCR |
| GenBank accession numbers for ammonia oxidizer genes collected on the R/V Endeavor (SQO-Delta) in the San Francisco Bay Delta during September and October 2007. | Genes quantified using gene-specific SYBR qPCR assays
| StepOnePlus Real-Time PCR System |
| Potential nitrification rates and ammonia oxidizer gene abundances collected on R/V Endeavor (SQO-Delta) in the San Francisco Bay Delta during September and October 2007 | Genes quantified using gene-specific SYBR qPCR assays
| StepOnePlus Real-Time PCR System |
| 454 pyrotags for Eukaryote taxa in deep hypersaline anoxic basin (DHAB) halocline sediments collected on R/V Atlantis cruise AT18-14 in the Eastern Mediterranean (35.3 N, 21.7 E) in 2011 | | Thermal Cycler |
| 454 pyrotags for Bacterial and Archaeal taxa in deep hypersaline anoxic basin (DHAB) halocline sediments from the R/V Atlantis AT18-14 cruise in the Eastern Mediterranean; 35.3 N 21.7 E in 2011 (Pickled Protists project) | | Thermal Cycler |
| Diatom amplicon sequencing variants (ASVs) from Narragansett Bay, Rhode Island, USA from 2008-2014 | | Eppendorf Mastercycler EP Gradient |
| Pseudo-nitzschia species microbiome identification collected from the Santa Cruz Warf in 2011 (bacteria, virus, diatom interactions project) | GeneAmp 2700 PCR system (Applied Biosystems, Foster City, CA) was used for PCR amplification.
| GeneAmp 2700 PCR system |
| DNA microsatellite alleles from eelgrass ramets collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014 | | |
| DNA microsatellite alleles from flowering shoots and seeds collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014 | | |
| Zooplankton community abundances from meter net tows on multiple cruises on RV/Savannah in the South Atlantic Bight, Mid-Continental Shelf from 2015-2017 | | Bio-Rad T100Thermocycler |
| Pallenopsis patagonica specimen and outgroups with accessions, from Table 1, Domel et al, in review, Frontiers in ...(Antarctic Inverts project) | | |
| Accession numbers for clone and Illumina amplicon sequence libraries from Dorado Outcrop basalts collected on R/V Atlantic cruise AT26-09 in December 2013 | | |
| NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014 | Florenciella 18S rRNA was amplified by PCR then cloned and extracted using the Zyppy Plasmid Miniprep Kit (Zymo Research).
| PCR |
| Iron and vitamin B12 metatranscriptomincs co-limitation in sea water collected from the Ross Sea in 2014 (Ross Sea Microb Ecophys project) | Life Technologies AccuPrime PCR system
Life Technologies ProFlex PCR system
| |
| Location, weathering, bulk isotope, and 14C data for fossil seals from the western Ross Sea, Antarctica from from 2013-2014 | | |
| Microbial gene abundance of coastal wetland soil cores collected in June 2018 from Barataria Bay, Louisiana | The number of gene copies for each sample was determined through qPCR analysis on a CFX96 Touch Real-Time PCR Detection System
| CFX96 Touch Real-Time PCR Detection System |
| Gnathiid blood meal identification results | A Veriti 96 Well Thermal Cycler (Applied Biosystem, Foster City, CA) was used to carry out PCR reactions with the following thermocycling conditions: initial denaturation step of 94 °C for 2 min, 30 cycles of 96 °C for 20 s, 55 °C for 20 s, and 72 °C for 45 s, and a final extension step of 72 °C for 7 min.
| Veriti 96 Well Thermal Cycler |
| Genotype data for E. lori individuals sequenced at 71 microsatellites from a 41 km-long transect of the Belize Barrier reef during 2018 | individuals were sequenced at 71 microsatellite loci using a multiplex PCR protocol for targeted amplicon sequencing.
| multiplex PCR protocol |
| Haloptilus longicornis population structure (Atlantic Ocean) - Microsatellite data. | PCR products were genotyped
| ABI3730 Genetic Analyzer |
| Antarctic invertebrate collection locations and NCBI SRA accessions from Halanych and Kocot (2014) Biol Bull (Antarctic Inverts project) | | |
| Best toll-like receptors (TLR) genes from Lophotrochozoa BLASTP search, from Table 3, Halanych and Kocot (2014) Biol. Bull. (Antarctic Inverts project) | | |
| Best other leucine-rich repeat (LRR) genes from Lophotrochozoa BLASTP search, from Table 4, Halanych and Kocot (2014) Biol. Bull. (Antarctic Inverts project) | | |
| GenBank accession numbers used in phylogenetic analysis in Table S1, Halanych et al (2013) Nature Comm. (Antarctic Inverts project) | | |
| Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata (Plankton Population Genetics project) | | |
| Sea spider Pallenopsis sampling sites and COI NCBI accessions from Table 1, Harder et al (2016) Polar Biology (Antarctic Inverts project) | | |
| Novel cyclooxygenase (COX) and peroxidasin (PXDN) sequences analyzed in Havird et al (2015) J Mol Evol., Table 1 (Antarctic Inverts project) | | |
| Data pertaining to the development of larvae past the planula stage from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Data pertaining to dose-response curves (DRC) quantifying survival of larvae after exposure to heat ramps from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Expression of heat shock protein 70 (HSP70) in larvae at 11 days post-fertilization (DPF) from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Heat tolerance (survival) of juveniles at 6 WPF following heat shock from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Lethal temperature 50s (LT50s) displayed by larvae derived from dose-response curves after heat shock from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Long-term body column lengths and tentacle numbers of larvae and juveniles from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Respiration rates and protein content of larvae from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Sizes of larvae from 4-11 days post-fertilization from experiments investigating heat priming in Nematostella vectensis | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers |
| Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project) | AB-7500 real-time QPCR system [ThermoFisher (Applied Biosystems), Waltham, MA, USA], with the following cycling conditions: 94◦ C for 10 min, followed by 40 cycles of 94◦C for 15 s, 60◦C for 1 min, and 72◦C for 15 s.
| ThermoFisher QPCR system |
| Host-symbiont respiration related to symbiont density; anemones from Key Largo from (AnemoneOA project) | AB-7500 real-time QPCR system [ThermoFisher (Applied Biosystems), Waltham, MA, USA], with the following cycling conditions: 94◦ C for 10 min, followed by 40 cycles of 94◦C for 15 s, 60◦C for 1 min, and 72◦C for 15 s.
| ThermoFisher QPCR system |
| Illumina sequencing data from sediment strata collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin | | |
| Biological, physical, and chemical data from surface Transect 5 on MV1405 (IRN-BRU) | Amplicon sequencing: PCRs were performed on a Life Technologies SimpliAmp Thermal Cycler and sequencing was performed using an Illumina MiSeq desktop sequencer.
| Life Technologies SimpliAmp Thermal Cycler |
| Isolation of microbes from hadal water and sediments from Mariana and Kermadec trenches from R/V Falkor, R/V Thomas G. Thompson FK141109, TN309, FK141215, April to December 2014 (Mariana Perspectives project) | | |
| Diatom ribosomal DNA sequence accession numbers from samples collected from the Eastern and Western Pacific and from the Western Atlantic between 2007 and 2009 (Diatom Gene Flow project) | | Thermocycler |
| Outgroup species, description reference, and GenBank accession numbers from Table 2, from Janosik & Halanych (2013) (Antarctic Inverts project) | | |
| Matrix of Odontasteridea morphological characters, Table 3 from Janosik & Halanych (2013) (Antarctic Inverts project) | | |
| Population analysis and metagenomics of Japanese tsunami marine debris mussels along the Hawaii, Washington and Oregon coasts in 2012 (JTMD-BF project) | | Thermal Cycler |
| Restriction site-associated DNA sequence metadata of Kelletia kelletii collected in California, USA and Baja, Mexico in 2015 to 2017 | Briefly, genomic DNA was digested using the isoschizomer restriction enzymes MboI and Sau3AI (New England Biolabs, Ipswich, MA). Digestions were performed in a total volume of 50 µl, containing 25 µl of dsDNA (~1 µg), 5 µl of NEB Cutsmart Buffer (provided with restriction enzymes), 18 µl of HPLC grade water, 1 µl MboI (10 units), and 1 µl Sau3AI (10 units) under the following thermocycler profile: 37 ºC for 18 h, then deactivation at 65 ºC for 20 min.
| thermocycler |
| Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Oceanus and R/V Urania (OC454-02) in the eastern Mediterranean Sea in 2009 (Pickled Protists project) | | PCR |
| Euphausiid DNA barcode metadata and accession numbers collected from cruises in the Red Sea, the western North Atlantic, the Sargasso Sea, the Southeast North Atlantic Ocean, and Arabian Sea (Red Sea Krill project) | | |
| Data describing Long-term PaV1 lobster surveys in the south-central Florida Bay from 1999-2014 (Lobster disease connectivity project) | | pCR |
| OTU molecular abundances for coral Symbiodinium, Belize Mesoamerican Barrier Reef System (MBRS), 2014-2015 | | |
| Genotype of symbionts detected in Orbicella faveolata recruits inoculated with either Symbiodinium microadriaticum, S. minutum or control (McIlroy,J. Phycology, 2016) (SymBioSys project) | | |
| Laboratory results: Genotypes of symbionts detected in Orbicella faveolata recruits of different ages and different history of symbiont exposure (McIlroy/Coffroth Coral Reefs, 2017) (SymBioSys project) | | |
| Information about the offspring used in a study of survival of Menidia menidia larvae under high CO2 conditions; conducted at Southampton Marine Station from 2011-2015 | | Thermal Cycler |
| Genotyped parents used in a study of survival of Menidia menidia larvae under high CO2 conditions; conducted at Southampton Marine Station from 2011-2015 | | Thermal Cycler |
| NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) | | quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology) |
| Metabarcoding zooplankton at station ALOHA: Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU (Plankton Population Genetics project) | | quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology) |
| Iberian Margin Anaerobic Sediment Metagenomes from R/V JOIDES Resolution cruise JRES-339 in the West Iberian margin from 2011-2012 (Subseafloor Microbial Ecology project) | | |
| NCBI accession numbers for metagenomic sequences collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project) | Bio-Rad C1000 Touch Thermocycler
| |
| Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Urania cruise in the Mediterranean Sea during 2012 (Pickled Protists project) | | Thermal Cycler |
| Microbial 16S OTU count data from staghorn coral health experiments with treatment with and without antibiotics | | |
| Microbial 16S OTU annotation information from staghorn coral health experiments with treatment with and without antibiotics | | |
| Sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs | | |
| Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016 | | |
| High throughput tag-sequencing accessions (18S rRNA gene region) and environmental metadata from Axial Seamount, 2013-2015 | | |
| High throughput tag-sequencing data from Gorda Ridge Hydrothermal vent field, including 16S and 18S rRNA gene sequences, and environmental metadata from Gorda Ridge Seamount, May/June 2019 | | |
| Microbial diversity and geochemistry of marine sediment mesocosm, Cape Lookout Bight, North Carolina | | |
| Microsatellite primer sequences from Pollicipes elegans collected at the University of Hawaii during 2015 (Gene flow across the tropics project) | | |
| Mitochondrial COI barcode sequencing data for Gigantidas childressi veligers, pediveligers, and juveniles from samples collected on R/V Thompson cruise TN391 in Mississippi Canyon 853 in the Gulf of Mexico during May 2021 | | PCR amplification |
| Cytochrome oxidase I DNA sequences from Pollicipes elegans collected at the University of Hawaii in 2015 (Gene flow across the tropics project) | | |
| Environmental measurements and high throughput sequencing data from samples collected at Martha's Vineyard Coastal Observation (MVCO) from 2013-2017 | | |
| Relative abundances of different Syndiniales groups from surface water samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly between 2013 and 2021 | | PCR |
| Larval heat tolerance of Nematostella vectensis following parental exposure to ocean acidification during lab experiments conducted in spring 2022. | MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) for thermal tolerance heat ramps
| MiniAmp thermal cyclers (Thermo Fisher Scientific, Waltham, MA, USA) |
| Nitrite reductase genes sequence accessions from the 2004 R/V Endeavor RMP Sediment Cruise in San Francisco Bay (N-Cycling Microbial Communities project) | Genes quantified using gene-specific SYBR qPCR assays
| StepOnePlus Real-Time PCR System |
| DNA microsatellite alleles for hatchery-produced oyster cohorts | | T100 thermal cycler (Bio-Rad) |
| Performance traits (e.g., survival, growth, size) for hatchery-produced oyster cohorts | | T100 thermal cycler (Bio-Rad) |
| Prevalence and intensity of oyster parasite species following a reef restoration experiment in Quonochontaug Pond, Rhode Island, USA from 2017-2020 | Bio-Rad CT100 thermal cycler – used for PCR analysis of oyster microparasites
| Bio-Rad CT100 thermal cycler |
| Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata (Plankton Population Genetics project) | | |
| Specimen log with OTU identifiers collected from Palau marine lakes | | |
| Voucher summary of invertebrates and barcoded OTU's with field identifications, collected from Palau marine lakes | | |
| Fungal iTAG analyses on Peru Margin sediment core samples from R/V JOIDES Resolution cruise JRES-201 in the Peru Margin from January to March 2002 | | |
| Planktonic ciliate DNA sequence GenBank accession numbers for samples collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project) | | |
| Analysis of temporal dynamics of three virus types persistently co-infecting Pleurochrysis carterae CCMP645 from laboratory experiments at the Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016 | Reactions were run on a Bio Rad icycler and data was analyzed following Bio Rad’s Instruction Manual, Catalog Number 170-8740.
| Bio Rad icycler |
| mtORF haplotype of each Pocillopora colony sampled at a given site and depth at Moorea, French Polynesia in August 2019 | | PCR amplification |
| Summary of Symbiodinium assemblages observed in Briareum asbestinum recruits reared at field sites in the Florida Keys each month, 1999-2002 (Fig. 2, Poland et al 2013) (SymBioSys project) | MJ Research PTC-100
| Thermal Cycler |
| Number of Briareum asbestinum juveniles with single (1 type) or multiple (2-6 types) simultaneous Symbiodinium populations in Florida Keys reefs, 1999-2002 (Fig. 3 in Poland et al 2013) (SymBioSys project) | MJ Research PTC-100
| Thermal Cycler |
| Number of Briareum asbestinum juveniles at 4 sites with a given Symbiodinium type over time (months) during 1999-2002 (Fig. 2, Poland et al 2013) (SymBioSys project) | MJ Research PTC-100
| Thermal Cycler |
| Genotype data for the three adult barnacle aggregations collected at the University of Hawaii in 2015 (Gene flow across the tropics project) | | |
| Larval genotype data for Pollicipes elegans collected at the Universtiy of Hawaii in 2013 (Gene flow across the tropics project) | | |
| The eukaryotic (poly-A) metatranscriptome for Canterbury Basin from R/V JOIDES Resolution cruise JRES-317 in the Canterbury Basin from 2009-2010 | | |
| DNA sequence data deposited on GenBank for polychaetes used in the project studying the evolution and mechanics of burrowing in La Jolla, CA during 2011 (Burrowing polychaete mechanics project) | | Thermal Cycler |
| Prochlorococcus or Synechococcus cell concentrations and nitrite concentrations during batch culture with ammonium or nitrate as the sole nitrogen source for growth | | CFX96 Thermocycler (Bio-Rad, Hercules, CA, USA) |
| Culture-independent identification of bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1 from R/V Falkor cruise FK141215 in the Challenger Deep, Mariana Trench in December 2014 | Multiple displacement amplification and 16S rRNA gene PCR and sequencing were performed
| |
| Pseudo-nitzschia spp. presence-absence and environmental data in Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023 | | Eppendorf Mastercycler EP Thermal Cycler Series |
| Pleuromamma xiphias mitochondrial genetic data (Atlantic; mtDNA) for analyses of population structure across the Atlantic Ocean | Polymerase Chain Reaction (PCR) amplification of a 681-bp fragment of mtCOI was conducted with primers and PCR and sequencing protocols as described in (Goetze, 2011).
| PCR |
| Quantitative PCR data from sediment samples from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project) | Genomic DNA was extracted from Baltic Sea Basin sediments using FastDNA® Spin Kit for Soil
(MP Biomedicals). 16S rRNA gene copy numbers of targets were quantified with qPCR using the
primers in the table in datasheet. Results of qPCR were rejected if the R2 of the standard curve was
below 0.95, or if the melt curve showed evidence of primer dimers. SYBR green chemistry was used
for all reactions, and Invitrogen mastermix was used for DNA copy number measurement on a
BioRad iQ5 (Applied Biosystems, Foster City, California). Serial dilutions of full-length 16S rRNA
gene PCR products from plasmids containing amplified partial 16S genes were used as standards.
BioRad iQ5
| BioRad iQ5 |
| Quantitative PCR data from sediment samples from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project) | Genomic DNA was extracted from Baltic Sea Basin sediments using FastDNA® Spin Kit for Soil
(MP Biomedicals). 16S rRNA gene copy numbers of targets were quantified with qPCR using the
primers in the table in datasheet. Results of qPCR were rejected if the R2 of the standard curve was
below 0.95, or if the melt curve showed evidence of primer dimers. SYBR green chemistry was used
for all reactions, and Invitrogen mastermix was used for DNA copy number measurement on a
BioRad iQ5 (Applied Biosystems, Foster City, California). Serial dilutions of full-length 16S rRNA
gene PCR products from plasmids containing amplified partial 16S genes were used as standards.
FastDNA® Spin Kit for Soil
| FastDNA® Spin Kit for Soil |
| qPCR data for archaeal amoA ecotypes; samples collected on METZYME cruise. | | |
| qPCR data from B/O Hermano Gines cruises in the CARIACO Basin Time Series Station from May to November 2014 (CariacoMetaOmics project) | All qPCR assays were performed on this thermal cycler using the SYBRgreen filter.
| Mx3000P thermal cycler (Agilent) |
| Quantitative PCR data from samples collected on the R/V Sarmiento de Gamboa cruise in the subtropical North Atlantic Ocean between January and March 2011 (Microbial associations in zooplankton project) | Used to process PCR samples
| PCR |
| Raw LC-MS/MS data, with list of identified peptides, and DNA sequences from a proteomic profile of Mariprofundus ferrooxydans | | |
| Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020 | The V4 region of the 16S rRNA gene was amplified using 515F and 806RB primers from total DNA, then barcoded, purified, and sequenced (Apprill et al., 2015; Parada et al., 2016).
| Thermocycler |
| The genotypes from 9 microsatellites generated on individuals of the red invasive seaweed Gracilaria vermiculophylla | Loci were amplified on a thermocycler (BioRad). The PCR program included 2 min at 95 degrees C, 30 cycles of 30 s at 95 degrees C, 30 s at 55 degrees C and 30 s at 72 degrees C, and a final 5 min at 72 degrees C.
| Thermocycler |
| Ostracod species from the Sargasso Sea collected on NOAA Ship Ronald H. Brown (RHB0603) in April 2006 (CMarZ_2004-2010 project) | Applied Biosystems 9600 Thermal cycler or in a Perkin Elmer 480 thermal cycler using the Gotaq Flexi DNA polymerase (Promega)
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| Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project) | | |
| Link to NCBI BioProject on programmed cell death from RVIB Nathaniel B. Palmer NBP1302 in the Ross Sea from February to April 2013 (TRACERS project) | | |
| Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project) | A PCR product ∼500 bp was generated, followed by development of internal primers to produce a smaller PCR product amenable to qPCR.
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| Dilution batch-culture bioassay (remineralization) experiments from SBDOM11 project cruise from R/V Point Sur PS1103 in the Santa Barbara Channel, May 2011 (SBDOM project, SBC LTER project) | used to conduct multiplex amplicon pyrosequencing
| |
| Identity of sciaenid eggs collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022 | | Aria Mx Real-Time PCR System, Agilent Technologies |
| Application of a rapid microbiome characterization pipeline to corals afflicted with Stony Coral Tissue Loss Disease in St. Thomas, US Virgin Islands. | | mini8 (miniPCR, Cambridge, MA, USA)and BentoLab (Bento Bioworks Ltd, London, UK) |
| Site descriptions and physical environmental conditions in coral microbiomes in the Florida Keys during 2013 (Coral Microbial Relationships project) | Reactions carried out on a Bio-Rad thermocycler (Bio-Rad Laboratories, Inc., Hercules, CA, USA)
| Bio-Rad thermocycler |
| DNA barcode sequencing results for bivalve larvae collected on N. Atlantic cruises at cold seeps sites off of Barbados, the East coast of the U.S. and the Gulf of Mexico (SEEPC project) | | Bio-Rad C1000 Touch Thermal Cycler |
| Sequence data accession numbers originating from coral and coral mucus mesocosm experiments conducted at the Bermuda Institute of Ocean Sciences in 2013 | Reactions carried out on a Bio-Rad thermocycler.
| Bio-Rad thermocycler |
| Single amplified genomes (SAGs) of chemoautotrophs from global deep sea samples (Dark ocean chemoautotrophs project) | | Roche LC480 |
| Metadata and accessions for comparative single-cell genomics of Chloroflexi from the Okinawa Trough deep subsurface biosphere from DV/Chikyu OIDP stations, Sept-Oct. 2010 (Subsurface FeOBs project) | Genetic analyses performed at Single Cell Genome Center (SCGC) at Bigelow Laboratory for Ocean Sciences
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| LC-MS/MS sequenced proteins extracted from Stylophora pistillata skeleton; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) | Amplifications were performed in a Veriti Thermal Cycler (Applied Biosystems) at 35 cycles of 98 degrees C for 10 s, primer-specific annealing temperature for 30 s, and 72 degrees C for 30–180 s. PCR products were sequenced by GENEWIZ.
| Veriti Thermal Cycler (Applied Biosystems) |
| Environmental data, nitrifier abundance, ammonia oxidation rates from six from R/V Savannah cruises in the South Atlantic Bight in 2014 (GCE-LTER) | C1000 Touch Thermal cycler (Bio-Rad Laboratories, Hercules, CA)
| C1000 Touch Thermal cycler |
| Accession numbers for raw sequence reads; samples collected on R/V Roger Revelle cruise KNOX02RR in the South Pacific Gyre from 2006-2007 (Microbial Diversity SPG project) | Samples were amplified using PCR, targeting the V4 region of the 16S rRNA gene. All amplifications were performed using the FastStart High Fidelity PCR System (Roche).
| PCR |
| soxB gene sequence data from microbial mats; collected on R/V Atlantis cruise AT18-08 at the Axial Seamount, Juan de Fuca Ridge in 2011 | | |
| SPOT Microbial Observatory Protist 18S rDNA TRFLP relative peak abundance data from 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project, Mar. Microbial Communities project) | | Thermal Cycler |
| SPOT Microbial Observatory Myovirus g23 3' TRFLP relative peak abundance data from 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project, Mar. Microbial Communities project) | | Thermal Cycler |
| SPOT Microbial Observatory Myovirus g23 5' TRFLP relative peak abundance data from 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project, Mar. Microbial Communities project) | | Thermal Cycler |
| SPOT Microbial Observatory Bacterial ARISA relative peak abundance data from 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project, Mar. Microbial Communities project) | | Thermal Cycler |
| Roseobacter isolate Sulfitobacter sp. CB2047 and three of its infecting phage accessions at NCBI GenBank | DNA Engine Thermo cycler (PTC-200)
| |
| Accession numbers of symbiotic algae in coral collected from the Florida Keys, Bahamas, Panama, and Mexico during 2010 (SymBioSys project) | Stratagene Mx3005P QPCR System (Stratagene, La Jolla, CA.)
| Thermal Cycler |
| Laboratory results on symbiont type in recovering Porites divaricata corals collected from the Florida Keys, Bahamas, Panama, and Mexico during 2010 (SymBioSys project) | Stratagene Mx3005P QPCR System (Stratagene, La Jolla, CA.)
| Thermal Cycler |
| Diatom (Thalassiosira pseudonana) cell information from experiments designed to study single-cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms conducted in December of 2022 | | C1000 Touch PCR Thermocycler, Biorad (Hercules, CA) |
| Diatom (Thalassiosira pseudonana) gene information from experiments designed to study single-cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms conducted in December of 2022 | | C1000 Touch PCR Thermocycler, Biorad (Hercules, CA) |
| Data from common garden experiment containing three populations of T. rotula | | |
| T. rotula microbiome global sample | | |
| Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices. | Specific information on primer sequences, PCR reaction mixes, thermal cycler conditions, and PCR purification is provided in the manuscript associated with this submission.
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| COI mtDNA sequences for trematodes from fish collections across the Northern Line Islands and French Polynesia archipelagos collected between 2009 and 2023 | Fisherbrand thermocyclers
| Fisherbrand thermocyclers |
| Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata | | |
| BioProject accession information for Trichodesmium colonies from R/V Atlantic Explorer AE1409, R/V Kilo Moana KM1513 and other cruises in the N. Atlantic, S. Pacific and N. Pacific, 2007-2015 (P Processing by Tricho project) | | |
| V3-V4 16S sequence accessions from samples of whole Gigantidas childressi as well as seafloor water samples collected on R/V Thompson cruise TN391 in Mississippi Canyon 853 in the Gulf of Mexico during May 2021 | | PCR amplification |
| V4 amplicon sequencing of coral tissue collected from Micronesia, the Florida Keys, and Australia in 2013 (Coral Microbial Relationships project) | Reactions carried out on a Bio-Rad thermocycler (Bio-Rad Laboratories, Inc., Hercules, CA, USA)
| Bio-Rad thermocycler |
| Partial SSU rRNA genes of bacteria and archaea from reef seawater samples produced using 515F/806R and 515F/806RB primers from the Bermuda, Red Sea, and Federated States of Micronesia in 2013 (Coral Microbial Relationships project) | Bio-Rad thermocycler (Bio-Rad Laboratories, Inc., Hercules, CA, USA)
| |
| Toxin genes identified in Nemertean species, Table 3 from Whelan et al (2014) Genome Bio & Evol.(Antarctic Inverts project) | Used to amplify full-length cDNA
| Advantage 2 PCR system (Clontech) |
| Whole community (3 domain) metatranscriptomes for subsurface sediment core samples from R/V JOIDES Resolution cruises JRES-201 and JRES-317 in the Peru Margin and Canterbury Basin in 2002 and 2009-10 | | |
| Whole genome sequence data for Pisaster ochranceus samples collected from the Pacific coast of North America from July 2004 to May 2018 | Following addition of A-tails, the DNA fragments were ligated to Illumina Truseq adaptors and again purified with AMPure beads. Amplification was achieved in a 50 μl reaction using PhusionTM High-Fidelity polymerase (Thermo Scientific) according to the manufacturer’s protocol and the following PCR thermocycler specifications: an initial 95 °C for 2 min, then 98 °C for 30 s, followed by 15 cycles of 98 °C for 15 s, 60 °C for 30 s, 72 °C for 4 min and a final 10 min incubation at 72 °C.
| PCR thermocycler, Bio-RAD T100 |
| Microbial culture collection, strain IDs, locations and depths R/V F.G. Walton Smith (WS1209) cruise in the Yucatan Carribean and Mexico during 2012 (CEMSB project) | | |
| Abiotic and biotic data from Zostera Experimental Network (ZEN) 2014 surveys (ZEN 2 project) | | |
| Biomass and diversity measurements in eelgrass (Zostera marina) habitat from 16 sites across the Northern Hemisphere, 2011 (ZEN project) | | |
©2020 Biological and Chemical Oceanography Data Management Office.