| 16S and 18S rRNA gene amplicon sequence links and metadata from microbial mesocosms spiked with 2-heptyl-4-quinolone (HHQ) experiments, Bergen, Norway, May 2017 | | Illumina MiSeq |
| Metagenetic amplicon sequence data for multiple coral species from Curacao, Australia and Hawaii | Genomic DNA and RNA were extracted and sequenced using Illumina MySeq
| Illumina MySeq |
| 16S microbiome metadata collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021 | Illumina MiSeq - sequencer used to generate sequence libraries from prepared samples
| Illumina MiSeq |
| 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) | Illumina MiSeq
| |
| 16S rRNA gene and particulate monooxygenase diversity from R/V Atlantis AT15-68, AT18-10, AT15-44, AT15-59 off Costa Rica and USA, Pacific Ocean, 2009-2011 (Authigenic Carbonate Ecosystems project) | | Automated Sequencer |
| 16S rRNA gene (from RNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010 | | Illumina MiSeq 2500 |
| GenBank accession numbers for microbial 16S rRNA sequences collected at the East Pacific Rise by DSV/Alvin during R/V Atlantis research cruises (Jan. 2004 - June 2006) (Microbial Communities at Deep-Sea Vents project) | | Capillary 3730xl DNA analyzer (Applied Biosystems) and 454 FLX Technology |
| 16S rRNA sequences for outplanted Acropora cervicornis sexual recruits collected from Mote Marine Laboratory and Looe Key National Marine Sanctuary from 2020-2022 | Illumina MiSeq
| |
| 16S V4 rRNA gene tag sequences from reef seawater samples collected in the Florida Keys and the U.S. Virgin Islands in 2019-2020 | | iSeq 100 System (Illumina) |
| NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 | | Illumina MiSeq |
| 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) | Sequencing was performed at the Institute for Genomic Medicine Genomics Center (University of California, San Diego, La Jolla, CA).
| Illumina Miseq |
| Field collection data for taxa detected in Copepod nauplii guts analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | ABI 3130 Genetic Analyzer
| Automated Sequencer |
| Taxa detected in field caught nauplii guts analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | ABI 3130 Genetic Analyzer
| Automated Sequencer |
| GenBank BLAST results of copepod nauplii gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | ABI 3130 Genetic Analyzer
| Automated Sequencer |
| Identification of copepod gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project) | ABI 3130 Genetic Analyzer
| Automated Sequencer |
| 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 | | Illumina MiSeq |
| 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 | | Illumina MiSeq platform |
| Sequences from the coral Acropora cervicornis determined before and after bleaching at the Mote Marine Laboratory in August and September 2015 | | Illumina MiSeq |
| Acropora cervicornis transcriptomes: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022 | | Illumina Nova Seq 6000 |
| Acropora cervicornis genomic/trancriptomic sequence accessions with associated data on tank exposure to white band disease and survival outcomes with corals collected from Florida, USA and Bocas del Toro, Panama in 2021 | | NovaSeq S4 |
| Acropora cervicornis genomic/trancriptomic sequence accessions with associated data on tank exposure to white band disease and survival outcomes with corals collected from Florida, USA and Bocas del Toro, Panama in 2021 | | Minion flow cells (FLO-MIN112) |
| Acropora cervicornis genomic/trancriptomic sequence accessions with associated data on tank exposure to white band disease and survival outcomes with corals collected from Florida, USA and Bocas del Toro, Panama in 2021 | | Illumina HiSeq 2500 |
| Acropora cervicornis genomic/trancriptomic sequence accessions with associated data on tank exposure to white band disease and survival outcomes with corals collected from Florida, USA and Bocas del Toro, Panama in 2021 | | Illumina NEXTSEQ 550 |
| Acropora palmata genotypes derived from microsatellite markers collected from multiple reefs in the Florida Keys National Marine Sanctuary from 2005-2014 (Surviving Climate Change project) | Applied Biosystems 3730 DNA Analyzer
| automated sequencer |
| Multilocus microsatellite genotypes of Acropora palmata from the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project) | | automated sequencer (ABI 3730) |
| Mutations at microsatellite loci of Acropora palmata in the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project) | | automated sequencer (ABI 3730) |
| Symbiodinium genotypes derived from microsatellite markers collected from multiple reefs in the Florida Keys National Marine Sanctuary from 2005-2014 (Surviving Climate Change project) | Applied Biosystems 3730 DNA Analyzer
| automated sequencer |
| Methodology information and links to data access for allele frequencies and FST estimates for 1,904,119 SNPs analyzed in five population samples of Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007 | Illumina HiSeq 2000 with paired-end 125 bp (for samples from GA, NY, GoM, and GSL)
| Illumina HiSeq 2000 |
| Methodology information and links to data access for allele frequencies and FST estimates for 1,904,119 SNPs analyzed in five population samples of Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007 | Illumina NextSeq500 paired-end 75 bp (for samples from NC).
| Illumina NextSeq500 |
| Accessions for clones of heterotrophic "helper" bacterium Alteromonas EZ55 grown at elevated and ambient CO2. | Used to prepare the mRNA libraries. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).
| Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA) |
| GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of Alviniconcha species from R/V Falkor in the Lau Basin from April to May 2016 | 16S rRNA genes were amplified from the extracted DNA with the 515F/926R primers (Walters et al., 2015) and PE 251bp reads were sequenced using Illumina MiSeq.
| Illumina MiSeq. |
| 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 | Manufactured by Illumina, Inc., San Diego, CA, USA
| Illumina MiSeq Next Generation Sequencing |
| 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) | | Illumina HiSeq Platform |
| 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) | Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA) at the core genomics center at University of Pennsylvania.
| |
| Genetic accession numbers for viral and bacterial metagenomes from Asteroid sea stars including sea star wasting disease state and collection information from sites worldwide between 2013 and 2016 (Sea Star Microbiology project) | | Illumina MiSeq Sequencer |
| 16S rRNA gene amplicon sequences from FLOCS experiments at the Juan de Fuca Ridge CORKs during August 2014. | Concentrated extracts were cleaned with the CleanAll DNA/RNA Clean Up and Concentration Kit (Norgen Biotek Corp, Thorold, Canada) and eluted in 20-50 μl of PCR-grade water. Sequencing of the V1-V3 region of the 16S rRNA gene was performed by Research and Testing Laboratory (Lubbock, TX, USA) using the forward primer 28F (5′- GAG TTT GAT CNT GGC TCA G -3′) and reverse primer 388R (5’- TGC TGC CTC CCG TAG GAG T -3’) for Bacteria using 2 x 300 bp kits on the Illumina MiSeq platform.
| Illumina MiSeq |
| 16S rRNA gene amplicon sequences from cathodic poised potential experiments with subsurface crustal samples from CORK borehole observatories at North Pond on the Mid-Atlantic Ridge during R/V Atlantis cruise AT39-01 | Aliquots of DNA extracts were sent to the Integrated Microbiome Resource facility at Dalhousie University (Halifax, Canada) for sequencing of the V4-V5 hypervariable region of the 16S rRNA gene via Illumina Mi-Seq technology using the 515F/926R primer pair. Sequencing was performed on an Illumina MiSeq using 300 300 bp paired-end V3 chemistry.
| Illumina MiSeq |
| Atlantic silverside (Menidia menidia) cDNA transcriptome and TSA accessions from specimens collected at Poquott Beach, New York in June of 2013 (Fishery Genome Changes project) | | Illumina HiSeq 2000 |
| NCBI accession numbers and associated metadata for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals | | Illumina HiSeq 2000 |
| Sample and genetic accession information for RNA-seq data from whole Atlantic silverside (Menidia menidia) larvae from two populations and their F1 hybrids reared under different temperatures in 2017 | Illumina HiSeq 4000 sequencer at BGI Genomics
| Illumina HiSeq 4000 |
| Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish collected on the north shore of Mo’orea, French Polynesia, Oct 2020 | DNA was extracted from all samples using the ZymoBIOMICS DNA/RNA Miniprep kit (Zymo Research, CA) according to the manufacturer’s instructions, but with a 1hr proteinase K incubation (35°C) before the lysis buffer step. Library preparation and sequencing was conducted at the Genomics Core Lab at the Institute of Arctic Biology of the University of Alaska Fairbanks. All samples were sequenced using the 16S rRNA gene V4 primers 515f (GTGYCAGCMGCCGCGGTAA) and 806rB (GGACTACNVGGGTWTCTAAT) on Illumina MiSeq using v3 2x300bp chemistry.
| Illumina MiSeq |
| Genotypes of symbionts in Muricea atlantica, M. elongata, and Plexaurella dichotoma across the 2015 Bleaching event (May 2015-August 2017) in the Florida Keys | Fragment analysis was performed on a LI-COR NEN Global IR2 DNA Sequencer.
| LI-COR NEN Global IR2 |
| Metadata associated with genomic and genetic data collected from organisms obtained on BOWLs landers, R/V Oceanus June 22-27, 2014 (BOWLS project) | Used for the RADSeq 50 bp data
| Illumina SE |
| Metadata associated with genomic and genetic data collected from organisms obtained on BOWLs landers, R/V Oceanus June 22-27, 2014 (BOWLS project) | Used for the mitochondrial and endosymbiont genome 150bp data
| Illumina PE |
| 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 | Fragment analysis of the PCR product of the microsatellite loci were run a on a 25 cm long, 0.25 mm thick, 6.5% non-denaturing polyacrylamide gel on an automated LI-COR 4200 NEN Global IR2 DNA sequencing system (LI-COR Biosciences).
| I-COR 4200 NEN® Global IR2 DNA sequencing system (LI-COR Biosciences) |
| Accession numbers for metagenome-assembled genomes (MAGs) from samples collected in 2018 on R/V Thompson cruise TN350 at the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano | Illumina HiSeq 3000: Sequencing platform used to generate metagenome reads
| Illumina HiSeq 3000 |
| 16S rRNA sequences from subsurface microbial communities (Blackwood Sinkhole) | Amplicons (100-200 ng) were sent to the Texas A&M AgriLife Bioinformatics and Genomics facility for library preparation with the Amplicon library preparation kit (Illumina) and sequencing with Illumina MiSeq with 250 bp paired-ends.
| Illumina MiSeq |
| Sampling and experimental metadata related to 'Candidatus' Aquarickettsia rohweri transcriptome data from host Acropora cervicornis colonies collected at Looe Key, Lower Florida Keys from Apr to Jun of 2019 | Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform: used for sample sequencing
| Illumina HiSeq 3000 platform |
| Links to a microarray and transcriptome for C. finmarchicus in the Gulf of Maine from 2008-2011 (CFINTRANSCRIPT project) | HiSeq2000 Illumina sequencer, in conjunction with Trinity software. Located at the Alpha Hudson Institute for Biotechnology, Huntsville, Alabama.
| Automated Sequencer |
| Coastal eastern subtropical pacific | llumina MiSEQ (v2 chemistry, paired 250 bp reads)
| llumina MiSEQ |
| Hemichordata and Echinodermata NCBI accessions, Table 2, Cannon et al (2013) Biol. Bull. (Antarctic Inverts project) | | Illumina MiSeq (San Diego, CA) at Auburn University |
| Hemichordata and Echinodermata GenBank accessions, Table S2, Cannon et al (2014) Curr. Bio. (Antarctic Inverts project) | | Illumina MiSeq (San Diego, CA) at Auburn University |
| Caribbean wide survey of PaV1 prevalence in adult lobsters in lobster fishing grounds from 2006-2007 and 2010-2011 (Lobster disease connectivity project) | ABI 3130 Prism Genetic Analyzer
| |
| Samples sequenced from chemosynthetic biofilm communities in deep-sea hydrothermal vents collected on the R/V Atlantis AT26-10 in the East Pacific Rise, Pacific Ocean from 2013 - 2014 (Microbial Communities at Deep-Sea Vents project) | Ion Torrent next-generation sequencing platform
| Automated Sequencer |
| Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016 | | Illumina MiSeq |
| Coral 16s rRNA sequence accession, sample, and experimental treatment information from white plague disease exposed corals at Brewer’s Bay, St. Thomas, The U.S. Virgin Islands in June of 2017 | | Illumina MiSeq 2x250bp PE reads |
| Coral associated microbes on coral, sediment, and water sampled from coral reefs in Mo'orea, French Polynesia from 2017 to 2020 | Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University.
| Illumina MiSeq platform |
| cDNA expressed sequence tags for the corals Acropora palmate and Orbicella faveola in Mexico, Panama, and the Florida Keys in 2003 (SymBioSys project) | | |
| RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016. | | Illumina HiSeq 2500 |
| Coral colony genetic sequence accession numbers for samples collected from the lagoon environment of Ofu Island, American Samoa between 2011 and 2015. | | Illumina HiSeq 2500 |
| Microbial ESV counts for Acropora millepora corals exposed to Galaxaura seaweed | 500-cycle paired-end MiSeq Reagent V2 Kit (Illumina).
| MiSeq sequencer |
| Microbial ESV counts for Acropora millepora corals exposed to Sargassum seaweed | 500-cycle paired-end MiSeq Reagent V2 Kit (Illumina).
| MiSeq sequencer |
| Accession numbers and images of coral samples taken in the Florida Keys during 2013 (Coral Microbial Relationships project) | MiSeq (Illumina, San Diego, CA, USA)
| MiSeq |
| Illumina sequenced 16S rRNA genes amplified from the different life stages of 2 corals in Kaneohe Bay, Oahu, Hawaii during 2010 (MiCoDe project) | Illumina MiSeq desktop sequencer
| |
| 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) | ABI 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA)
| |
| 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) | ABI 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA)
| |
| Diel, daily, and spatial variation of coral reef seawater microbial communities from US Virgin Islands, 2017 | Used to obtain genetic data.
| Miseq (Illumina, San Diego, CA) sequencer |
| Specificity of associations between bacteria and Pocillopora meandrina during early development in Kaneohe Bay, Oahu, Hawaii from 2008 (MiCoDe project) | ABI 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA)
| |
| T-RFLP, response of the microbial community to coral spawning, lagoon and reef flats in Kaneohe Bay, Oahu, Hawaii during 2006 - 2007 (MiCoDe project) | ABI 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA)
| |
| Eastern oyster gonad methylation patterns in response to experimental ocean acidification | Paired-end 100bp DNA sequencing was performed on the Illumina HiSeq1500 system.
| Illumina HiSeq1500 |
| Nucleotide sequences of CsRV1 virus amplified from blue crabs (Callinectes sapidus) from coastal waters and estuaries in North and South America, including the Caribbean and Gulf of Mexico from 2006 to 2020 | Illumina MiSeq
| |
| Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016 (Host Symbiont Temp Response project) | DNA was amplified using the primers HYPERUP and HYPERDN on and MJ96 thermocycler and PCR products were visualized and scored using size standards on the LI-COR 4200 NEN® Global IR2 DNA sequencing system as specified in Santos et al (2003).
| LI-COR 4200 NEN® Global IR2 DNA |
| Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016 (Host Symbiont Temp Response project) | The B7SYM15 flanking region was amplified and directly sequenced in 5’ and 3’ directions on a 3730XL DNA Analyzer (High Throughput Genomics Center, University of Washington).
| 3730XL DNA Analyzer |
| Population genomics study on the planktonic pteropod Cuvierina spp.: RADSeq data and metadata (Plankton Population Genetics project) | | Illumina HiSeq 2500 |
| Genbank accession numbers for genome sequences of cyanomyoviruses collected from the coastal waters of North America | Illumina HiSeq2000 sequencer (single read, paired-end with 100 cycles) at the UCI Genomics High-throughput Facility or Illumina MiSeq at the Rhode Island Genomics and Sequencing Center at the University of Rhode Island.
| |
| 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) | Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).
| |
| 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) | Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).
| |
| Philine spp. collection data and NCBI accessions links for 16S haplotype sequences from Krug et al (2012) Biol. Invasions (PLDvFST project) | Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).
| |
| 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) | Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).
| |
| 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) | Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).
| |
| Molecular species delimitation and gene flow in Oxynoe (PLDvFST project) | Big Dye Terminator 3.1 Cycle Sequencing chemistry Retrogen, Inc. (San Diego)
| Automated sequencer |
| 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 | cDNA amplicons were sequenced on a GS-FLX Titanium 454 sequencer at EnGenCore (University of South Carolina, Columbia, SC), which resulted in ~37000 reads.
| GS-FLX Titanium 454 sequencer |
| 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 | Roche 454 FLX Titanium platform
| Automated Sequencer |
| 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) | Roche 454 FLX Titanium platform
| Automated Sequencer |
| Diatom amplicon sequencing variants (ASVs) from Narragansett Bay, Rhode Island, USA from 2008-2014 | | Illumina MiSeq platform |
| Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture | | HiSeq Illumina 2500 |
| Pseudo-nitzschia species microbiome identification collected from the Santa Cruz Warf in 2011 (bacteria, virus, diatom interactions project) | A Seqman II (version 9.0 DNASTAR Inc, Madison, WI, USA) was used for sequencing of bacterial 16s rDNA.
| Seqman II |
| Pseudo-nitzschia species microbiome identification collected from the Santa Cruz Warf in 2011 (bacteria, virus, diatom interactions project) | Genome Sequencer FLX System was used for pyroseqencing of pseudo-nitzschia microbiome.
| Genome Sequencer FLX System |
| A study using amplicon sequencing of the viral mcp gene of dinoRNAVs to analyze their dynamics in the reef-buliding coral Porites c.f. lobata at three reef zones around Moorea, French Polynesia | | Illumina MiSeq |
| Acropora cervicornis coral disease exposure experiment conducted on Summerland Key, FL from August to September of 2015 (Resilient Acerv project) | Snips, approximately 2 cm in size, were taken from two random replicates within each genotype for Symbiodinium sequencing. Preliminary analyses indicate that all genotypes contain only A3 clade symbiodinium, but they may harbor different genotypes of the symbiont. These samples were flash frozed at -80C and stored until processing. DNA was isolated and extracted from 2 - 3 polyps worth of tissue using the Qiagen DNAeasy DNA isolation kit. Samples will be sent to Dr. Iliana Baums at Penn State University for microsatellite analysis and identification of possible variations in symbiont genotypes within coral genets.
| Qiagen DNAeasy DNA isolation kit |
| DNA and cDNA (RNA) V4 tag sequence genetic accessions from microbial eukaryotes sampled in the upper euphotic zone of the eastern North Pacific during R/V Yellowfin cruises from 2003-2018 | | Illumina MiSeq |
| DNA microsatellite alleles from eelgrass ramets collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014 | | 3730xl Genetic Analyzer (Applied Biosystems) |
| DNA microsatellite alleles from flowering shoots and seeds collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014 | | 3730xl Genetic Analyzer (Applied Biosystems) |
| Zooplankton community abundances from meter net tows on multiple cruises on RV/Savannah in the South Atlantic Bight, Mid-Continental Shelf from 2015-2017 | | |
| Pallenopsis patagonica specimen and outgroups with accessions, from Table 1, Domel et al, in review, Frontiers in ...(Antarctic Inverts project) | Sequencing performed at High Throughput Genomics Center (Seattle, WA) and at GATC Biotech AG (Cologne, Germany)
| |
| DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013 | | Illumina HiSeq platform |
| Bacterial 16S rRNA sequences from hydrothermal plume particles sampled at 9 degrees North, East Pacific Rise, depth 2500m, on R/V Atlantis cruise AT15-06 in July 2006. | Applied Biosystems Automated DNA Sequencer
| |
| Bacterial 16S rRNA sequences from inactive sulfide chimneys from R/V Atlantis cruise AT11-20 in the North East Pacific Rise in November 2004 | Automated DNA Sequencer, Applied Biosystems and Roche 454 GS20 DNA Sequencer
| Applied Biosystems |
| Microsatellite genotypes, and cytb sequences for Etelis coruscans, Etelis carbunculus, and Etelis sp. and sample collection information in the Indo-Pacific Ocean from 1997 and 2012 | ABI 3730XL or ABI 3130XL genetic analyzers
| |
| Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278 | Libraries were sequenced on an Illumina HiSeq 2500.
| Illumina HiSeq 2500 |
| Accession numbers of viral metagenomes from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013 | | Illumina HiSEq 2000 |
| NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014 | DNA was sequenced using Illumina (NextSeq System) and PacBio methods.
| Illumina (NextSeq System) |
| NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014 | DNA was sequenced using Illumina (NextSeq System) and PacBio methods.
| PacBio P6 C4 |
| Pool-seq data from laboratory selection lines of copepods collected from Kiel Canal in Germany in 2017 and 2018 | | Illumina Hi-Seq 4000 and Illumina NovaSeq 6000 |
| Pool-seq data from wild populations of copepods in the Baltic Sea from May 2018 through August 2019 | | Illumina HiSeq 4000 sequencer |
| Microbiome composition of coral species collected from reefs in Mo'orea, French Polynesia and exposed to various experimental treatments in August 2018 | Sequencing was performed on the Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University.
| Illumina MiSeq platform |
| Incubation experiments were conducted in St. John, US Virgin Islands to investigate the response of reef seawater microbial communities to the mixed exudates released from the coral species Porites astreoides and Gorgonia ventalina. | Illumina iSeq 100 sequencer
Illumina MiSeq sequencer (2x250 bp)
| Illumina sequencers |
| Iron and vitamin B12 metatranscriptomincs co-limitation in sea water collected from the Ross Sea in 2014 (Ross Sea Microb Ecophys project) | Illumina HiSeq platform
| |
| Fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State between Mar of 2019 and Jan of 2020 | | 3730xl Genetic Analyzer with the LIZ-500 size standard |
| Symbiodinium species and relative abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract, April 2014 (EMUCoReS project) | | Illumina Mi-Seq - MR.DNA Next Generation Sequencing, Shallowater, Texas (www.mrdnalab.com) |
| Symbiodinium species and relative abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract, 2015-2016 (EMUCoReS project) | | Illumina Mi-Seq - MR.DNA Next Generation Sequencing, Shallowater, Texas (www.mrdnalab.com) |
| GenBank accession numbers and links for microbial isolates from sediment samples collected in Paleochori Bay, Milos Island, Greece during 2012 (Hydrothermal Autotrophic Carbon Fixation project) | Ion Torrent platform
| |
| Costa Rica Margin Subseafloor Microbial Community Analysis | | Illumina HiSeq 1000 system |
| Evolutionary and acclimatory shifts in gene expression of Eurytemora affinis copepods reared in saline and freshwater conditions during laboratory experiments from 2011-2014 | Libraries were sequenced on an Illumina HiSeq platform at the University of Maryland, School of Medicine, Institute for Genome Sciences.
| Illumina HiSeq 2000 |
| Gene expression of Pocillopora damicornis collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021 | Sequencing was completed targeting standard coverage of 3–5 million 100-bp single-end reads per sample (Illumina NovaSeq 600 SR100).
| Illumina NovaSeq 600 SR100 |
| Genetic accession numbers and sampling information for metaviromes collected during the R/V Thomas G. Thompson cruise TN-280 along Line P in the northeast Pacific Ocean in May of 2012 | | Illumina HiSeq 2500 |
| GenBank Short Read Archive (SRA) sequence accession numbers for 16S rRNA gene amplicon in the Eastern Lau Spreading Center, Lau Basin from R/V Falkor from March to April 2016 | 16S rRNA genes were amplified from the extracted DNA with the 515F/926R primers (Walters et al., 2015) and PE 251bp reads were sequenced using Illumina MiSeq.
| Illumina MiSeq. |
| Glaucus atlanticus sample locations, museum voucher and GenBank accession numbers from in a global sample set (Neuston Phylogeny project) | ABI 3730xl (Applied Biosystems, Inc.)
| Automated Sequencer |
| Glaucus Study II: locality data, GenBank and museum voucher numbers, with molecular synapomorphies from a global sample set (Neuston Phylogeny project) | ABI 3730xl (Applied Biosystems, Inc.)
| Automated Sequencer |
| Glaucus specimen collection locations, museum vouchers and GenBank accession numbers from a global sample set (Neuston Phylogeny project) | ABI 3730xl (Applied Biosystems, Inc.)
| Automated Sequencer |
| Protein sequences from diversity-generating retroelements in groundwater microorganisms collected near Rifle, Colorado between 2011 and 2012 (Viruses in Methanotrophic Marine Ecosystems project) | | Illumina HiSeq 2000 |
| Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019 | Desktop sequencer
| Illumina Next-Seq 500 |
| Antarctic invertebrate collection locations and NCBI SRA accessions from Halanych and Kocot (2014) Biol Bull (Antarctic Inverts project) | | Illumina (San Diego, CA) HiSeq 2000 platform at The Genomic Services Lab at the Hudson Alpha Institute in Huntsville, Alabama, |
| Best toll-like receptors (TLR) genes from Lophotrochozoa BLASTP search, from Table 3, Halanych and Kocot (2014) Biol. Bull. (Antarctic Inverts project) | | Illumina (San Diego, CA) HiSeq 2000 platform at The Genomic Services Lab at the Hudson Alpha Institute in Huntsville, Alabama, |
| Best other leucine-rich repeat (LRR) genes from Lophotrochozoa BLASTP search, from Table 4, Halanych and Kocot (2014) Biol. Bull. (Antarctic Inverts project) | | Illumina (San Diego, CA) HiSeq 2000 platform at The Genomic Services Lab at the Hudson Alpha Institute in Huntsville, Alabama, |
| GenBank accession numbers used in phylogenetic analysis in Table S1, Halanych et al (2013) Nature Comm. (Antarctic Inverts project) | | Illumina MiSeq (San Diego, CA) at Auburn University |
| Population genomics study on the planktonic copepod Haloptilus longicornis: RADSeq data and metadata (Plankton Population Genetics project) | | Illumina HiSeq 2500 |
| Accession numbers for planktonic ciliate haplotypes collected on R/V Lowell Weicker in the Long Island Sound in 2008 | Samples were sequenced in either an ABI 3000 automated sequencer or in an ABI 377 automated sequencer.
| Automated Sequencer |
| Sea spider Pallenopsis sampling sites and COI NCBI accessions from Table 1, Harder et al (2016) Polar Biology (Antarctic Inverts project) | Sequencing performed at High Throughput Genomics Center (Seattle, WA)
| |
| Novel cyclooxygenase (COX) and peroxidasin (PXDN) sequences analyzed in Havird et al (2015) J Mol Evol., Table 1 (Antarctic Inverts project) | | Illumina MiSeq (San Diego, CA) at Auburn University |
| Reef Fish genetic accessions at NCBI Genbank from samples collected in the Indian Ocean, Pacific Ocean, and Red Sea from 2005 to 2015; related to 2016 publications | ABI 3730XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA)
| ABI 3730XL Genetic Analyzer |
| NCBI accessions of the harmful alga Heterosigma akashiwo (CCMP2393) grown under a range of CO2 concentrations from 200-1000 ppm | Used to prepare the mRNA libraries. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).
| Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit (Illumina, San Diego, CA) |
| Results of 18S sequencing of full-length 18S rDNA for metabarcoding samples collected during R/V Point Sur cruise PS18-09 in the Western Gulf of Mexico in September 2017 | Library construction and amplicon sequencing was performed at Campbell Lab, Texas A&M University using Oxford Nanopore minION.
| Oxford Nanopore minION Mk1C |
| Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017. | Used to obtain DNA sequences. See https://www.illumina.com/systems/sequencing-platforms/miseq.html
| Illumina MiSeq |
| Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey | | Illumina Hiseq 2500 platform |
| GenBank accession links of the invertebrates collected from Autonomous Reef Monitoring Structures (ARMS) from shallow fringing reefs near Dobu and Upa Upasina, Milne Bay Province, Papua New Guinea in 2014 | ABI 3130xl: Laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions.
| ABI 3130xl |
| Supplementary Table 4B: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes | RNA sequencing was performed using the Illumina NextSeq 550 platform (Univ. of Georgia).
| Illumina NextSeq 550 platform |
| Supplementary Table 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences, FPKM values | RNA sequencing was performed using the Illumina NextSeq 550 platform (Univ. of Georgia).v
| Illumina NextSeq 550 platform |
| Supplementary Table 4C: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data. | DNA sequencing performed using the Illumina MiSeq 2 x 300 bp platform (Univ. of Georgia)
| Illumina MiSeq 2 x 300 bp platform |
| 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.
| Illumina MiSeq desktop sequencer |
| 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) | Sequencing was done on an ABI ABI 3130xL (Applied Biosystems) genetic analyzer.
| ABI 3130xL (Applied Biosystems) |
| Outgroup species, description reference, and GenBank accession numbers from Table 2, from Janosik & Halanych (2013) (Antarctic Inverts project) | Purified products were then sequenced bidirectionally
| Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter) |
| Matrix of Odontasteridea morphological characters, Table 3 from Janosik & Halanych (2013) (Antarctic Inverts project) | Purified products were then sequenced bidirectionally
| Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter) |
| Sample log from Jason-II dives for Sievert collected from the R/V Atlantis (AT26-10) in the East Pacific Rise, Pacific Ocean (Microbial Communities at Deep-Sea Vents project) | | |
| Population analysis and metagenomics of Japanese tsunami marine debris mussels along the Hawaii, Washington and Oregon coasts in 2012 (JTMD-BF project) | Ion Torrent platform
| DNA sequencer |
| SSU rRNA gene sequences from marine sediments, marine subseafloor, and deep seawater sampled from the Juan de Fuca Ridge Flank from various R/V Atlantis cruises from 2008-2011 (microJdFR project) | Clones were sequenced unidirectionally on an ABI 3730XL DNA Analyzer (Applied Biosystems, Carlsbad, CA).
| ABI 3730XL DNA Analyzer |
| Pyrosequencing reads (454) of marine RNA virus metagenomes collected Kaneohe Bay, HI during 2009 (Diversity and ecology of marine RNA viruses project) | GS FLX Titanium platform (Roche Diagnostics Corporation)
| |
| Flow cytometry, 16S rRNA gene amplicons, chlorophyll a, and surface seawater measurements taken between August 2017 to June 2019 Kāneʻohe Bay, Oʻahu, Hawaiʻi | | Illumina MiSeq v2 |
| Biological oceanographic measurements, 16S rRNA gene amplicons and metagenomes from surface seawater taken from August 2017 to June 2021 at sites within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi | Amplicon sequencing
| Illumina MiSeq v2 |
| Biological oceanographic measurements, 16S rRNA gene amplicons and metagenomes from surface seawater taken from August 2017 to June 2021 at sites within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi | Metagenome sequencing
| NovaSeq 6000 SP 150 |
| Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii | | Nanopore MinION |
| Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii | | PacBio sequel 2 |
| Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii | | ILLUMINA |
| 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) | Roche 454 FLX Titanium platform
| Sequencer |
| 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) | | |
| Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount; from R/V Roger Revelle and R/V Thomas G. Thompson cruises RR1211 and TN225 in the Northeast Lau Basin, Loihi Seamount from 2008-2012 | | Illumina HiSeq 2000 sequencer |
| Bacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides) collected on R/V Thomas G. Thompson cruise TN235 in the Eastern Lau Spreading Center from May to June 2009 | Applied Biosystems
| Automated DNA Sequencer |
| Whole genome sequence data from bacterial isolates from venting fluids at NW Rota Seamount, collected on R/V Thomas G. Thompson and R/V Kilo Moana cruises TN232 and KM1005 in the Mariana arc of the western Pacific in 2009 and 2010 | Libraries were prepared using Nextera DNA sample prep kits (Illumina, San Diego, CA, USA) and sequenced by Roche 454 GS FLX Titanium (454 Life Sciences, Branford, CT, USA) and/or using Illumina HiSeq 2000 paired reads (Illumina).
| |
| Analysis protocols, sample information, code, and datasets associated with the manuscript Structure and long-term stability of the microbiome in diverse diatom cultures from samples collected in Guam, California, and Gulf of Mexico between 2008 and 2016 | | Illumina MiSeq platform |
| OTU molecular abundances for coral Symbiodinium, Belize Mesoamerican Barrier Reef System (MBRS), 2014-2015 | | Illumina Mi-seq |
| Genotype of symbionts detected in Orbicella faveolata recruits inoculated with either Symbiodinium microadriaticum, S. minutum or control (McIlroy,J. Phycology, 2016) (SymBioSys project) | | LI-COR Long ReadIR 4200 DNA Sequencer |
| 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) | | LI-COR Long ReadIR 4200 DNA Sequencer |
| Microbial taxa (amplicon sequence variant or ASV) statistical analyses for two seagrass genotypes from wasting disease mesocosm experiments at Bodega Marine Laboratory in July-Sept of 2015 | | Illumina MiSeq |
| NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) | Illumina MiSeq using V3 chemistry (300-bp, paired-end)
| Illumina MiSeq |
| Metabarcoding zooplankton at station ALOHA: Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU (Plankton Population Genetics project) | Illumina MiSeq using V3 chemistry (300-bp, paired-end)
| Illumina MiSeq |
| Incubation experiments were conducted in St. John, US Virgin Islands to investigate the response of reef seawater microbial communities to the specific metabolites riboflavin, pantothenic acid, and caffeine. | Illumina iSeq 100 sequencer
Illumina MiSeq sequencer (2x250 bp)
| Illumina sequencers |
| Metadata for RNASeq of green crabs collected in the northeast Pacific from Apr 2017 to Aug 2021 | Samples were sequenced using Illumina HiSeq4000 sequencers by Azenta (formerly Genewiz; South Plainfield NJ).
| Illumina HiSeq4000 sequencers |
| Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022 | Illumina NovaSeq X 10B sequencing (150 bp paired-end), conducted at University of California at Berkeley's QB3 Genomics Core lab
| Illumina NovaSeq X 10B |
| Metagenomic data from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010 | | Illumina HiSeq 2500 |
| Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities collected on cruises AT42-22, TN405, and NA108 from May 2019 to Jun 2022 | Libraries were sequenced with NovaSeq at the Northwest Genomics Sequence Center (Seattle, WA).
| Illumina NovaSeq 6000 |
| Sample and treatment information for the environmental metagenome of paired bleaching and nonbleaching Pocillopora cf. meandrina corals in Mo'orea, French Polynesia in March of 2016 | Sequencing was performed on the Illumina HiSeq 3000 sequencing platform at the Center for Genome Research and Biocomputing at Oregon State University.
| Illumina HiSeq 3000 |
| 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) | Illumina HiSeq
| |
| Data from nutrient manipulation experiments (conducted on EXPORTS cruise DY131) aimed at relieving or inducing nutrient stress in phytoplankton and quantifying these responses using metatranscriptomic sequencing | | Illumina NovaSeq 6000 platform |
| Data on microbial metatranscriptomics: Niskin vs. in situ sampler from the R/V Urania cruise in the Mediterranean Sea during 2012 (Pickled Protists project) | Illumina HiSeq system
| Sequencer |
| Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Urania cruise in the Mediterranean Sea during 2012 (Pickled Protists project) | Roche 454 FLX Titanium platform
| Automated Sequencer |
| Microbial 16S OTU count data from staghorn coral health experiments with treatment with and without antibiotics | | Illumina HiSeq 2500 |
| Microbial 16S OTU annotation information from staghorn coral health experiments with treatment with and without antibiotics | | Illumina HiSeq 2500 |
| Microbial alpha diversity of Acropora millepora samples from a coral-seaweed competition experiment in the Fiji Islands, Dec. 2014 | | Illumina MiSeq sequencer |
| 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 | | MiSeq 300 x 300 bp PE |
| 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 | | MiSeq 300 x 300 bp PE |
| 18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 2020 | | Illumina MiSeq |
| Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015 | HiSeq High Output 125 bp PE sequencing was performed at UPC Genome Core at University of Southern California, Los Angeles, CA (BioProject: PRJNA391503).
| HiSeq |
| Microbial diversity and geochemistry of marine sediment mesocosm, Cape Lookout Bight, North Carolina | Illumina MiSeq at the Center for Environmental Biotechnology at the University of Tennessee in Knoxville
| |
| Microbial isolates from sediment samples collected in Paleochori Bay, Milos Island, Greece during 2012 (Hydrothermal Autotrophic Carbon Fixation project) | Ion Torrent platform
| |
| Microbiome dynamics of coral reef and cleanerfish from ecological surveys, in situ manipulations, and laboratory experiments conducted from 2020-2021 | | Illumina MiSeq |
| Microbiome data from sponges collected in 2013 and 2014 from reefs in Honduras, Belize, Panama and the Florida Keys. | Microbiome sequencing was carried out on an Illumina MiSeq.
| Illumina MiSeq |
| Microsatellite primer sequences from Pollicipes elegans collected at the University of Hawaii during 2015 (Gene flow across the tropics project) | ABI 3100 sequencer at the Arizona State University DNA Lab
| |
| Eukaryote transcriptome assemblies and associated metadata available on iMicrobe (P-ExpEv project) | Pacific Biosciences RS and Illumina HiSeq 2000 at NCGR
| |
| Molecular identification of genetic variants of Neocalanus flemingeri in the Gulf of Alaska from samples collected from 2015 to 2023 | | Illumina MiSeq |
| Molecular identification of genetic variants of Neocalanus flemingeri in the Gulf of Alaska from samples collected from 2015 to 2023 | | Illumina Next-Seq 500 |
| Mollusc museum voucher and GenBank accession numbers from a global sample set (Neuston Phylogeny project) | ABI 3730xl (Applied Biosystems, Inc.)
| Automated Sequencer |
| Cytochrome oxidase I DNA sequences from Pollicipes elegans collected at the University of Hawaii in 2015 (Gene flow across the tropics project) | ABI 3100 sequencer at the Arizona State University DNA Lab
| |
| Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female from the R/V Tiglax and R/V Sikuliaq in the Northern Gulf of Alaska from 2015-2022 | Desktop sequencer. Illumina NextSeq 500 instrument using High-Output Flow Cell.
| Illumina NextSeq 500 |
| NCBI accession numbers for RNAseq data from five coral species experimentally exposed to Stony Coral Tissue Loss Disease (SCTLD) at the University of the Virgin Islands in 2019 | mRNA libraries underwent 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 instrument.
| Illumina NovaSeq 6000 |
| NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri | | Illumina HiSeq 2500 |
| RNAseq data from apparently healthy and Stony Coral Tissue Loss Disease-affected Montastraea cavernosa coral collected from St. Thomas, US Virgin Islands in 2020 | | Illumina NovaSeq 6000 |
| Gene expression profiles for Neocalanus flemingeri pre adults (CV) exposed to four different experimental food conditions collected from the M/V Dora in the Gulf of Alaska at station GAK1 from April 2019 | Desktop sequencer
| Illumina Next-Seq 500 |
| NCBI Accession number link to the closed genome of Nitrosopelagicus brevis CN25 (AmoA Archaea project) | | illumina sequencer |
| 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 | | Illumina MiniSeq |
| Nudibranch accession numbers from a global sample set (Neuston Phylogeny project) | ABI 3730xl automated sequencer (Applied Biosystems, Inc.)
http://www6.appliedbiosystems.com/products/abi3730xlspecs.cfm
| Automated Sequencer |
| Accession numbers from acidification mesocosms and original in situ samples from coastal and offshore water station at the Pivers Island Coastal Observatory January to February 2017 | The resulting cDNA libraries were sequenced (250-bp single-end reads) using the Illumina HiSeq 2500 sequencer at the Georgia Institute of Technology Genomics Facility.
| Illumina HiSeq 2500 sequencer |
| NCBI accession numbers describing 16S rRNA and 16S rRNA gene amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A | | Illumina MiSeq |
| 19 Metagenomes and 7 metatranscriptomes from sediment samples collected offshore of San Francisco, Califronia, USA | | Illumina NovaSeq 6000 |
| 19 Metagenomes and 7 metatranscriptomes from sediment samples collected offshore of San Francisco, Califronia, USA | | Illumina HiSeq 4000 |
| NCBI accession numbers describing nifH amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A | | Illumina MiSeq platform |
| Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 | | Illumina MiSeq |
| DNA microsatellite alleles for hatchery-produced oyster cohorts | | 3730xl Genetic Analyzer (Applied Biosystems) |
| Performance traits (e.g., survival, growth, size) for hatchery-produced oyster cohorts | | 3730xl Genetic Analyzer (Applied Biosystems) |
| Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata (Plankton Population Genetics project) | | Illumina HiSeq 2500 |
| 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 | Purified replicate PCR amplifications from each sample were combined prior to iTAG sequencing using Illumina MiSeq PE300 at Georgia Genomics Center.
| |
| 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) | Roche 454 platform and others
| |
| Genetic sequence accessions, collection information, and methodology for raw sequences from ezRAD libraries of Pocillopora spp. collected in Moorea, French Polynesia in 2019 | | Illumina MiSeq |
| 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) | LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA)
| Automated Sequencer |
| 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) | LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA)
| Automated Sequencer |
| 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) | LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA)
| Automated Sequencer |
| Genotype data for the three adult barnacle aggregations collected at the University of Hawaii in 2015 (Gene flow across the tropics project) | ABI 3100 sequencer at the Arizona State University DNA Lab
| |
| Larval genotype data for Pollicipes elegans collected at the Universtiy of Hawaii in 2013 (Gene flow across the tropics project) | ABI 3100 sequencer at the Arizona State University DNA Lab
| |
| 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) | Sequencing was done by either Retrogen (San Diego, CA) or Eurofins MWG Operon (Louisville, KY).
| DNA Sequencer |
| Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014 | Libraries were sequenced on an Illumina HiSeq platform at the University of Maryland, School of Medicine, Institute for Genome Sciences.
| Illumina HiSeq 2000 |
| A re-sampling of historical population genetic surveys of Zostera marina from Bodega, Tomales, and San Francisco Bays USA; study performed at Bodega Marine Laboratory in 2014-15 | We analyzed fragments on an ABI 3010XL at the UC Davis DNA sequencing facility, and visualized the fragments using STRand software (Toonen & Hughes 2001).
| ABI 3010XL |
| Prokaryote and eukaryote abundance in phytodetrital aggregates (PA), fecal aggregates (FA), and the ambient seawater from samples collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda | | Illumina MiSeq |
| Clones of Prochlorococcus MIT9312 mixed with clonal isolates of the heterotrophic "helper" bacterium Alteromonas EZ55 (P-ExpEv project) | Used to prepare the mRNA libraries. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).
| Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA) |
| Amplicon sequence variants (ASVs) recovered from samples and their related identification as Pseudo-nitzschia taxa and the methods used | | Illumina MiSeq Next Generation Sequencing (University of Rhode Island Genomics and Sequencing Center) |
| Pseudo-nitzschia species diversity, viral titers and environmental data collected semi-monthly in 2013-2014 in Puget Sound and the Washington coast | | Illumina HiSeq 2500 |
| Presence or absence of amplicon sequence variants (ASVs) recovered from samples which are described in DATASET 01, Pseudo-nitzschia spp. from weekly samples and offshore cruises with the Northeast U.S. Shelf (NES) Long-Term Ecological Research (LTER) | | Illumina MiSeq Next Generation Sequencing (University of Rhode Island Genomics and Sequencing Center) |
| 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 | Manufactured by Illumina, Inc., San Diego, CA, USA
| Illumina MiSeq Platform |
| Symbiodinium sequence abundance in St. John, US Virgin Islands from 1994-2010 (RUI-LTREB project) | ABI 3100 Genetic Analyzer (Perkin-Elmer Applied Biosystems)
| ABI 3100 Genetic Analyzer |
| Data resulting from testing dilution experiments conducted in the development of four assays to quantify copeod naupliar biomass in Kaneohe Bay, Hawaii | Applied Biosystems 3730XL, with BigDye terminator chemistry v3.1, was used for sequencing species and qPCR products.
| Applied Biosystems 3730XL |
| Measurements of mixed field samples used for qPCR estimates and estimating biomass of DNA copy number in bulk samples | Applied Biosystems 3730XL, with BigDye terminator chemistry v3.1, was used for sequencing species and qPCR products.
| Applied Biosystems 3730XL |
| 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 | Applied Biosystems 3730XL, with BigDye terminator chemistry v3.1, was used for sequencing species and qPCR products.
| Applied Biosystems 3730XL |
| RADseq data from Atlantic silversides used for linkage and QTL mapping. | | Illumina NextSeq500 |
| Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007 | Illumina HiSeq 2000 with paired-end 125 bp (for samples from GA, NY, GoM, and GSL)
| Illumina HiSeq 2000 |
| Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007 | Illumina NextSeq500 paired-end 75 bp (for samples from NC)
| Illumina NextSeq500 |
| Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters project) | An aliquot of 8 ng of product from each sample was pooled, purified using HiPrep beads (MagBio, Gaithersburg, MD, USA), and sequenced on a NextSeq SE150 Mid Output flow cell (SE150) at the Georgia Genomics and Bioinformatics Core Facility (Athens, Georgia, USA).
| NextSeq SE150 (Illumina, San Diego, CA, USA) |
| The genotypes from 9 microsatellites generated on individuals of the red invasive seaweed Gracilaria vermiculophylla | Samples were electrophoresed on an ABI 3130xL genetic analyzer equipped with 36 cm capillaries (Applied Biosystems).
| ABI 3130xL genetic analyzer |
| Biogeochemistry, metabolomics, and metagenomics of Florida's Coral Reef from sampling conducted over 15 days in June 2019 | Illumina MiSeq using paired-end 250 bp sequencing - for 16S rRNA gene sequencing libraries of bulk reef seawater
| Illumina MiSeq |
| Biogeochemistry, metabolomics, and metagenomics of Florida's Coral Reef from sampling conducted over 15 days in June 2019 | Illumina NextSeq 2000 with the P3 flow cell and paired-end 150 bp sequencing for shotgun metagenomics
| Illumina NextSeq 2000 |
| Biogeochemistry, metabolomics, and metagenomics of Florida's Coral Reef from sampling conducted over 15 days in June 2019 | Illumina iSeq 100 System (Illumina) with the i1 cartridge, and 2x150 bp sequencing for 16S rRNA libraries of coral and near-coral seawater
| Illumina iSeq 100 System |
| Reef Fish genetic accession numbers at NCBI Genbank | DNA barcodes (COI) were produced with an ABI 3130XL genetic analyzer (Applied Biosystems, Foster City, California).
| ABI 3130XL |
| Reef fish NCBI genetic sequence accession numbers for sequences from reef fish specimens collected in the Indo-Pacific and Pacific Ocean | DNA barcodes were produced with an ABI 3130XL genetic analyzer (Applied Biosystems, Foster City, California)
| ABI 3130XL genetic analyzer |
| Ostracod species from the Sargasso Sea collected on NOAA Ship Ronald H. Brown (RHB0603) in April 2006 (CMarZ_2004-2010 project) | Applied Biosystems 3130 capillary DNA Sequencer
| |
| Data relating to RNA sequence accessions at NCBI from Ross Sea Dinoflagellates, Phaeocystis antarctica, Pyramimons tychotreta, and Micromonas polaris (CCMP 2099) (Kleptoplasty project) | | Illumina Mi-Seq |
| NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015 | For genetic sequencing
| Illumina® HiSeq 2500 |
| RNAseq data used to identify Alphaflexivirus genomes in Stony Coral Tissue Loss Disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands (Multi-Species Coral Disease project) | An Illumina NovaSeq 6000 was used for 150-bp, pared-end mRNA sequencing
| Illumina NovaSeq 6000 |
| Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project) | Illumina MiSeq
| Automated Sequencer |
| Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project) | Used to sequence genomes
| Illumina MiSeq |
| 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) | | Illumina HiSeq 2500 platform |
| 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) | For genome sequencing
| Multiple sequencing platforms: Ion Torrent Proton (Life Technologies, Grand Island, NY), a 454 FLX WGS (Roche Applied Science, Branford, CT), and an Illumina HiSeq 200 (Illumina, San Diego, CA) |
| NCBI project accession and library information on each sample analyzed in upwelling experiments conducted on two phytoplankton species isolated from the California Upwelling Zone | Samples were sequenced on an Illumina MiSeq.
| Illumina MiSeq |
| Sample key for Symbiodinium species and abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract April - Dec. 2014 (EMUCoReS project) | | Illumina platform |
| Metadata from sediment samples collected at Paleochori Bay, Milos Island, Greece in 2012 (Hydrothermal Autotrophic Carbon Fixation project) | Ion Torrent platform
| |
| Cyanobacterial and diatom samples collecteced between April and September 2022, and sequenced for metabarcodig of 16S and rbcL. | | Illumina MiSeq |
| Sampling information and sequence accessions for 18S-V4 sequences from surface water collected at the Santa Monica Pier (SMP) Santa Monica Bay, CA from 2018 to 2019 | Instrument used for deciphering the order of bases in a strand of DNA.
| Illumina MiSeq |
| 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
| |
| Application of a rapid microbiome characterization pipeline to corals afflicted with Stony Coral Tissue Loss Disease in St. Thomas, US Virgin Islands. | | Illumina iSeq 100 System (Illumina Inc., San Diego, CA, USA) |
| We shipped DNA samples to Dalhousie University's IMR facility for library prep and Illumina MiSeq 300 bp sequencing according to (92).
| |
| Site descriptions and physical environmental conditions in coral microbiomes in the Florida Keys during 2013 (Coral Microbial Relationships project) | MiSeq (Illumina, San Diego, CA, USA)
| MiSeq |
| Accession numbers for Labyrinthulomycetes detected in sea fans collected in the Florida Keys and Puerto Rico from 2006-2010 (Climate_CoralDisease project) | Direct sequencing was performed at the Cornell University Life Sciences Core Laboratories on an Applied Biosystems Automated 3730 DNA Analyzer
| Automated DNA Sequencer |
| Accession numbers for Gorgonia ventalina (sea fan) sequencing data from samples collected in the Florida Keys and Puerto Rico from 2006-2010 (Climate_CoralDisease project) | Each library was sequenced using an Illumina/Solexa Genome Analyzer at the Cornell University Core Laboratory Center.
| Automated DNA Sequencer |
| Marine sediment trap metagenomes from R/V Kilo Moana KM1215, KM1219 in the Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii, July to September 2012 (C-MORE project) | MOBIO Powerwater
Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol.
| MOBIO Powerwater |
| Marine sediment trap metagenomes from R/V Kilo Moana KM1215, KM1219 in the Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii, July to September 2012 (C-MORE project) | Illumina Nextera XT
Illumina Nextera XT Data Sheet
Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol.
| Illumina Nextera XT |
| Marine sediment trap metagenomes from R/V Kilo Moana KM1215, KM1219 in the Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii, July to September 2012 (C-MORE project) | MiSeq instrument
This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.
| MiSeq instrument |
| 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) | The sequencing was done by Sequetech in California
| Applied Biosystems 3730xl DNA Analyzer |
| Sequencing reads_(2bRAD) for Montastrea cavernosa, Siderastrea siderea, Agaricia agaricites and Porites astreoides from Florida Reefs | | Illumina HiSeq 2500 |
| Gene copy number counts and 16S analyses of July 2019 Rhode River surface water incubated with or without viral dilution | | Illumina MiSeq |
| Water quality data, gene copy number counts, and 16S analyses from Rhode River samples collected at SERC during 2017 and 2018 | | Illumina MiSeq |
| Taxonomic binning of transcripts from samples collected during the SIMCO1 (July 2014) and SIMCO2 (Oct 2014) incubation experiments on the linkage between DOM changes and microbial transcription patterns at Sapelo Island, GA. | mRNA-enriched material was sequenced
| Illumina HiSeq2500 |
| Transcript counts per liter from samples collected during the SIMCO 1 & 2 (July & Oct 2014) incubation experiments on the linkage between DOM changes and microbial transcription patterns at Sapelo Island, GA. | mRNA-enriched material was sequenced
| Illumina HiSeq2500 |
| Metatranscriptome sequence NCBI accessions from samples collected during the SIMCO 1 & 2 incubation experiments, July & Oct 2014 | mRNA-enriched material was sequenced
| Illumina HiSeq2500 |
| Single amplified genomes (SAGs) of chemoautotrophs from global deep sea samples (Dark ocean chemoautotrophs project) | Used to read base pairs
| MiSeq and NextSeq 500 (Illumina) |
| 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
| |
| Sample information for 16S and 18S V4 amplicon sequencing of microbial communities in sinking particles and water column samples collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda | | Illumina MiSeq |
| 16S gene sequencing of microbial communities in South China Sea sediments from January to March 2014 | Paired-end 250-bp sequencing was performed on an Illumina MiSeq at Oregon State University’s Center for Genome Research and Biocomputing.
| Illumina MiSeq |
| NCBI accessions and metadata associated with Caribbean sponge metagenomes collected from Curacao, Belize, Cayman Islands and St. Croix, 2009 and 2017-2018 | | |
| Microbial Symbionts, Carbon, and Nutrient Cycling in Caribbean Coral Reef Sponges from Conch Reef, Key Largo (Florida, USA) and Carrie Bow Cay (Belize) in June and July 2016 | | Illumina MiSeq platform |
| SRA accessions and collection information for 16S-V4 rRNA amplicon data from invertebrates sampled at Flower Garden Banks National Marine Sanctuary, Gulf of Mexico following Tax Day Flooding (2016), Hurricane Harvey (2017), and a no flooding year (2018) | | Illumina MiSeq Platform |
| 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) | | Automated Sequencer |
| 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) | | Automated Sequencer |
| 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) | | Automated Sequencer |
| 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) | | Automated Sequencer |
| ssDNA-dsDNA viromes from the Great Lakes, off Bermuda and the South Pacific (GOV project) | | |
| A characterization of microbes at the San Pedro Ocean Time-series (SPOT) from 2005 to 2018, using SSU rRNA gene sequencing from two size fractions, with a universal primer set that amplifies from prokaryotes and eukaryotes | Purified PCR products were sequenced on an Illumina HiSeq 2500 in PE250 mode or MiSeq PE300.
| Illumina HiSeq 2500 sequencer |
| A characterization of microbes at the San Pedro Ocean Time-series (SPOT) from 2005 to 2018, using SSU rRNA gene sequencing from two size fractions, with a universal primer set that amplifies from prokaryotes and eukaryotes | Purified PCR products were sequenced on an Illumina HiSeq 2500 in PE250 mode or MiSeq PE300.
| Illumina MiSeq sequencer |
| Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates | | Illumina NextSeq 2000 |
| Roseobacter isolate Sulfitobacter sp. CB2047 and three of its infecting phage accessions at NCBI GenBank | Illumina HiSeq2000 at Center for Pediatric Genome Medicine Children's Mercy Hospitals and Clinics in Kansas City, MO.
| |
| Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study | Transcripts were sequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for Biotechnology (AL, USA).
| HiSeq Illumina 2500 |
| Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments | | Illumina MiSeq platform |
| An investigation of Symbiodiniaceae communities via ITS-2 rDNA amplicon sequencing in Acropora millepora corals from the Great Barrier Reef following exposure to stressors in October 2014 | ITS-2 rDNA Symbiodiniaceae community libraries were prepared and PE 300bp reads were generated using Illumina MiSeq platform
| Illumina MiSeq platform |
| Accession numbers of symbiotic algae in coral collected from the Florida Keys, Bahamas, Panama, and Mexico during 2010 (SymBioSys project) | LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA)
| Automated Sequencer |
| Laboratory results on symbiont type in recovering Porites divaricata corals collected from the Florida Keys, Bahamas, Panama, and Mexico during 2010 (SymBioSys project) | LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA)
| Automated Sequencer |
| NCBI accessions for raw genomic sequence data of 11 new isolates of marine Synechococcus from Naragansett Bay, July 2017 | Sequencing was done by Novogene (Beijing, China) on an Illumina 1500 making 2x150 pe reads.
| Illumina 1500 |
| Synechococcus (WH8102 and CC9311) growth and genetic sequence accessions from experiments with variable pCO2 treatments from 2016 to 2018 | | Illumina Hi-seq 2500 paired-end sequencing (PE100) |
| 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 | | Nextseq 500 DNA sequencer, Illumina (San Diego, CA) |
| Data from common garden experiment containing three populations of T. rotula | | Illumina MiSeq 2x250 bp PE reads |
| T. rotula microbiome global sample | | Illumina MiSeq 2x250 bp PE reads |
| ENA accessions for transcriptomes of T. oceanica and T. weissflogii grown in varied Fe and light (GeTFeHvCOdia project) | | |
| NCBI and iMicrobe accessions for transcriptomes of T. oceanica and T. weissflogii grown in varied Fe and light (GeTFeHvCOdia project) | | |
| Thalassiosira pseudonana CCMP1335 endometabolite uptake by Ruegeria pomeroyi DSS-3 | Illumina NovaSeq was used for transcriptome sequencing
| Illumina NovaSeq |
| Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification. | Used to identify samples
| Illumina NextSEQ 500 |
| Data and analysis code used to experimentally evolve representatives of four phytoplankton functional types in co-culture with a heterotrophic bacterium under either present-day or predicted future pCO2 conditions | | NextSeq500 (Illumina) |
| Flow cytometry and nutrient analyses data from a tidal study over 48 hours of mangrove, seagrass, and seawater from the US Virgin Islands in July of 2017 | Samples were shipped to the Georgia Genomics and Bioinformatics Core at the University of Georgia for sequencing on an Illumina MiSeq using paired-end 250bp sequencing
| Illumina MiSeq |
| Laboratory results containing transcripts of four cultivated marine bacteria from 2014-2015 (EAGER Respiration project) | | Illumina HiSeq 2500 |
| Transcriptomes of co-cultured marine microbes (Emiliania huxleyi, Thalassiosira pseudonana, and Synechococcus) and Ruegeria pomeroyi DSS-3 | | Illumina NovaSeq |
| NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ) | | llumina NextSeq500 |
| Genetic accessions, treatment information, and methodology from laboratory experiments studying transcriptomic responses to saxitoxin in zebrafish (Danio rerio) | | Illumina HiSeq 2000 |
| Transcriptomics of phytoplankton cultures grown on various phosphorus sources in a laboratory experiment | SAMN44278360 - SAMN44278371 (I. galbana) RNA-seq data were generated using the Illumina NovaSeq 6000 instrument at the University of New Hampshire.
SAMN44278372 - SAMN44278383 (E. huxleyi) RNA-seq data were generated using the Illumina NoveSeq Plus instrument at the University of Chicago.
SAMN44278384 - SAMN44278395 (M. pusilla) RNA-seq data were generated using the Illumina NoveSeq Plus instrument at the University of Chicago.
| Illumina NovaSeq 6000 |
| 16S sequence data in the form of fastq.gz files for all samples collected and sequenced as part of the Varadero Reef transplant experiment | | Illumina MiSeq sequencing platform |
| Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata | | Illumina Miseq platform |
| NCBI accessions for raw RNA-seq fastq in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California: deep metatranscriptomic sequencing of Trichodesmium enrichment cultures (HiCO2_AdaptCyano project) | Used to sequence the extracted RNA, performed at UC San Diego Institute for Genomic Medicine
| Illumina Hi-Seq |
| 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) | | Illumina Miseq platform |
| Seawater microbial communities within coral reef seawater change over six years in response to disturbance | | Illumina MiSeq |
| 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) | MiSeq (Illumina, San Diego, CA, USA)
| |
| Single amplified genomes (SAGs) of microbial cells isolated from deep-sea hydrothermal vent 'Crab Spa', East Pacific Rise, Pacific Ocean from R/V Atlantis AT15-38 and AT26-10, 2008 and 2014 (Microbial Communities at Deep-Sea Vents project) | MiSeq and NextSeq (Illumina) sequencers
| |
| Toxin genes identified in Nemertean species, Table 3 from Whelan et al (2014) Genome Bio & Evol.(Antarctic Inverts project) | | Illumina HiSeq 2000 at HudsonAlpha Institute for Biotechnology (Huntsville, AL) |
| Whole genome sequence data for Pisaster ochranceus samples collected from the Pacific coast of North America from July 2004 to May 2018 | Sequencing of WGS data was performed on Illumina NovaSeq sequencing machines.
| Illumina NovaSeq sequencing machines |
| Whole genome sequence data for Pisaster ochranceus samples collected from the Pacific coast of North America from July 2004 to May 2018 | Sequencing of WGS data was performed on Illumina NovaSeq sequencing machines. Some samples were sequenced at the UC Davis Sequencing Core (those from central California), the rest were sequenced at Novogene.
| Novogene |
| Sample collection information and sequence accessions at the National Center for Biotechnology Information (NCBI) for whole genome sequencing of eelgrass (Zostera marina) collected at Bodega and Tomales Bay, CA, USA from July to September 2019 | | NovaSeq 6000 S4 X |
| Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project) | Used to sequence pooled E. affinis samples.
| Illumina HiSeq 2000 sequencer |
| 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) | | |
| Sample collection and sequence accession information for Zostera marina whole genome resequencing from specimens collected at 16 geographic locations worldwide in 2017 | | Illumina HiSeq2500 sequencer |
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