Instrument: Thermal Cycler

Acronym:

Thermal Cycler

External Identifier:

» skos:closeMatch https://vocab.nerc.ac.uk/collection/L05/current/LAB50/ , http://purl.obolibrary.org/obo/OBI_0400116

Description

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Datasets

Dataset Name	Brief Description
16S microbiome data for artificial reef sponges and seawater	16S microbiome data for artificial reef sponges and seawater
16S rRNA accessions: IODP Site 1244	16S rRNA gene amplicon sequence accessions, Hydrate Ridge, offshore Oregon
16S rRNA gene Amplicon Library	16S rRNA gene Amplicon Library accession numbers
16S rRNA Sequences	16S rRNA sequence data from venting fluids and microbial mats at Axial Seamount, 2011.
16S V4 rRNA gene tag sequences from reef seawater	16S V4 rRNA gene tag sequences from reef seawater
515F-926R 16S rRNA accessions	515F-926R 16S rRNA accessions, Mariana and Kermadec trenches, 2014
5a_field collection	Field collection data for taxa detected in nauplii guts
5b_nauplii gut taxa	Taxa detected in field caught nauplii guts
5c_BLAST results	GenBank BLAST results of copepod nauplii gut contents
5d_molecular id of copepod guts	Identification of copepod gut contents
Accession numbers (P. carterae viruses and field samples)	Accession numbers for genetic sequences from virus-enriched field samples and P. carterae CCMP 645 culture co-infections
Acropora cervicornis 16S Sequences Metadata and NCBI SRA accessions associated with Williams et al., 2022	Acropora cervicornis 16S Sequences Metadata and NCBI SRA accessions associated with Williams et al., 2022
Acropora cervicornis bleaching sequences	Acropora cervicornis bleaching sequences
Acropora palmata genotypes for clonal age	Mutations at microsatellite loci of Acropora palmata
Acropora palmata mutations	Mutations at microsatellite loci of Acropora palmata
Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp.
Amplicon sequencing of ammonia oxidizing archaea amoA gene	Amplicon sequencing of ammonia oxidizing archaea amoA gene from cruise KM1314, Aug. 8 - Sept. 4, 2013 in the northern Pacific
AMT22 Population Samples	Overview of population samples included in genetic analyses of Pleuromamma xiphias
Anaerobic Peru Margin 2002	Sub-seafloor metatranscriptomes from anaerobic Peru Margin sediments collected on JOIDES Resolution, Leg 201.
Anaerobic Sediment 18S rRNA amplicons	Iberian Margin Anaerobic Sediment 18S rRNA amplicons.
ARISA relative abundances	ARISA relative abundances (bacterial community structure), San Pedro Channel, 5 depths
Assembled metagenome sequences > 500 bp	Assembled metagenome sequences > 500 bp from EPR, Lo'ihi, and control
BATS_Feb_Aug_2012_diversity_rDNA_BLAST	BLAST results from the Bermuda Atlantic Time Series (BATS) site in Feb. and Aug. 2012
BATS_Feb_Aug_2012_rDNA_sample_log	sample log for 16S and 18S rDNA amplicons sequenced with 454 technology, BATS site, 2012
Bleached octocoral genotypes	Bleached Octocoral Symbiont Cell Counts
Breviolum antillogorgium microsatellite loci	Microsatellite loci for B. antillogorgium cultures
Bugula neritina Genotype Distribution	Bugula neritina host genotype and symbiotic status of colonies along the East Coast
Cannon_2013_T2: NCBI accessions	Hemichordata and Echinodermata NCBI accessions
Cannon_2014_S2: Hemichordata and Echinodermata sample log and accessions	Hemichordata and Echinodermata transcriptome NCBI accessions
Caribbean PaV1 survey	Caribbean wide survey of PaV1 prevalence in adult lobsters, 2006-2007 and 2010-2011
CARP accession numbers	Sequence accession numbers for coral acid rich proteins (CARPs) from Stylophora pistillata.
Circovirus DNA Sequence Information	DNA sequences of viruses associated with Copepods
Community 16S rRNA gene sequences	16S rRNA accessions
Coral cDNA Expressed Sequences	cDNA Expressed Sequence Tags for the corals Acropora palmate and Orbicella faveola
Coral images and accession numbers	Species images and accession numbers for tissue, mucus, and holobionts analyzed.
coral life stages - Illumina	Illumina sequenced 16S rRNA genes amplified from different life stages of 2 corals
coral microbe T-RF - biogeography	Hawaiian coral terminal-restriction fragment length polymorphism (T-RFLP) analysis
coral microbe T-RF - temp stress	Terminal restriction fragments from 16S rRNA genes amplified from coral-associated microbes, response to temperature stress
Coral-bacterioplankton data from mesocosm experiments	Bacterioplankton data from coral and coral mucus aquaria experiments.
coral-microbe T-RF - development	Specificity of associations between bacteria and the coral Pocillopora meandrina during early development
coral-microbe T-RF - spawning	T-RFLP, response of the microbial community to coral spawning, lagoon and reef flats, Oahu, 2006-7
Cuvierina SRA	Cuvierina SRA, accessions, collection info
dataset2_Krug_et_al_2012: Elysia accessions	Elysia spp. accessions for COI, 16S, H3
dataset3_Supp1_Krug_et_al_2011: Elysia sequences	Accessions for COI, 16S, H3 for 18 Elysia species
dataset4_Krug_et_al_2012: Philine sequences	Accessions for 16S for Philine species
dataset5_Vendetti_et_al_2012: Elysia pusilla sequences	Accessions for COI, 16S, H3 from Elysia pusilla and E. spp.
dataset6_Krug_et_al_2013: Sequences	Accessions for COI, H3 for three species complexes
dataset8- Oxynoe sequence data	Species names, sample codes, and collection details for sequenced taxa used in phylogenetic analyses.
Deep Biosphere Eukaryotic rRNA	Sub-seafloor sediment eukaryotic rRNA collected on JOIDES Resolution Legs 201 and 204, R/V Maria Merian at North Pond, and R/V Meteor at the Benguela Upwelling System.
Delta Nitrification Study - GenBank Accession Numbers	GenBank accession numbers for ammonia oxidizer genes.
Delta Nitrification Study - Potential Nitrification Rates	Nitrification rates and ammonia oxidizer gene abundances
DHAB halocline sediment pyrotags - eukaryotes	454 pyrotags for Eukaryote taxa in deep hypersaline anoxic basin (DHAB) halocline sediments
DHAB halocline sediment pyrotags - prokaryotes	454 pyrotags for Bacterial and Archaeal taxa in deep hypersaline anoxic basin (DHAB) halocline sediments
Diatom amplicon sequencing variants from Narragansett Bay 2008-2014	Diatom amplicon sequencing variants from Narragansett Bay 2008-2014
Diatom microbiome	Identification of microbiome from different Pseudo-nitzschia species
DNA microsatellite alleles - Eelgrass ramets	DNA microsatellite alleles for eelgrass ramets from two sites in MA
DNA microsatellite alleles - Flowering shoots and seeds	DNA microsatellite alleles from flowering shoots and seeds
Doliolid diet: zooplankton abundance	Zooplankton abundances
Domel_2017_T1: Pallenopsis patagonica specimen and outgroups with accessions	Pallenopsis patagonica specimen and outgroups with accessions
Dorado Outcrop basalt DNA sequences	Accession numbers for clone and Illumina amplicon sequence libraries from Dorado Outcrop basalts
Eukaryotic viruses encode the ribosomal protein eL40	Eukaryotic viruses encode the ribosomal protein eL40
Fe_Vit12_MetaT_Co-Limitation_RossSea_2014	Iron and vitamin B12 metatranscriptomincs co-limitation in Ross Sea waters, 2014
Fossil Seal Bulk Isotopes 14C	Location, weathering, bulk isotope, and 14C data for fossil seals from the western Ross Sea, Antarctica
Gene Abundance
Gnathiid blood meal identification results
Goby_Sibship_2018	Genotype data for E. lori individuals sequenced at 71 microsatellites.
H. longicornis Population Structure
Halanych-Kocot_2014_T1: NCBI accessions	Antarctic invertebrate collection locations and NCBI SRA accessions
Halanych-Kocot_2014_T3: Best TLR genes from BLASTP search	Best toll-like receptors (TLR) genes from Lophotrochozoa BLASTP search
Halanych-Kocot_2014_T4: Best other LRR genes from BLASTP search	Best other leucine-rich repeat (LRR) genes from BLASTP search
Halanych_2013_T1: NCBI accessions	NCBI accessions
Haloptilus longicornis SRA	H. longicornis SRA, accessions, collection info
Harder_2016_T1: sea spider Pallenopsis sampling sites and COI NCBI accessions	Sea spider Pallenopsis sampling sites and COI NCBI accessions
Havird_2015_T1: NCBI accessions: COX and PXDN	NCBI accessions
Heat priming in Nematostella vectensis: Development of larvae past the planula stage	Heat priming in Nematostella vectensis: Development of larvae past the planula stage
Heat priming in Nematostella vectensis: Dose-response curves (DRC) quantifying survival after exposure to heat ramps	Heat priming in Nematostella vectensis: Dose-response curves (DRC) quantifying survival after exposure to heat ramps
Heat priming in Nematostella vectensis: Expression of heat shock protein 70 (HSP70)	Heat priming in Nematostella vectensis: Expression of heat shock protein 70 (HSP70)
Heat priming in Nematostella vectensis: Heat tolerance (survival) of juveniles	Heat priming in Nematostella vectensis: Heat tolerance (survival) of juveniles
Heat priming in Nematostella vectensis: Lethal temperature 50s (LT50s)	Heat priming in Nematostella vectensis: Lethal temperature 50s (LT50s)
Heat priming in Nematostella vectensis: Long-term growth	Heat priming in Nematostella vectensis: Long-term growth
Heat priming in Nematostella vectensis: Respiration rates and protein content of larvae	Heat priming in Nematostella vectensis: Respiration rates and protein content of larvae
Heat priming in Nematostella vectensis: Sizes of larvae	Heat priming in Nematostella vectensis: Sizes of larvae
Host-symbiont reinfections	Symbiont removed and anemone reinfected with one of two strains of Symbiodinium
Host-Symbiont respiration relationship	Host-symbiont respiration related to symbiont density; anemones from Key Largo
Illumina Sequences
IRN-BRU MV1405 Transect 5 BioGeoChem
Isolates	Isolates from Mariana and Kermadec trenches, 2014
ITS_sequence_accessions	Diatom ribosomal DNA sequence accession numbers.
Janosik_2013_T2: outgroup species and accessions	Outgroup species and accessions
Janosik_2013_T3: matrix of Odontasteridea morphological characters	Matrix of Odontasteridea morphological characters
JTMD Mytilus population genetics	Population analysis and metagenomics of Japanese tsunami marine debris mussels
kinetoplastid SSU rRNA seq.	Microbial metatranscriptomics: upper and lower halocline water column
Krill barcodes	Euphausiid DNA barcode metadata and accession numbers from global oceans
Long-term PaV1 survey	Long-term PaV1 lobster surveys Florida bayside, 1999-2014
MBRS Symbiodinium OTU	Symbiodinium OTU
McIlroy_2016: Symbionts genotypes in Orbicella faveolata	McIlroy_2016: Genotype of symbionts detected in Orbicella faveolata recruits over time
McIlroy_2017: Symbionts genotypes in Orbicella faveolata	McIlroy_2017: Genotype of symbionts detected in Orbicella faveolata recruits
Menidia menidia - Genotyped Offspring	Information about the offspring used in a study of survival of Menidia menidia larvae under high CO2 conditions.
Menidia menidia - Genotyped Parents	Genotyped parents used in a study of survival of Menidia menidia larvae under high CO2 conditions.
Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers	NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample
Metabarcoding zooplankton at station ALOHA: OTU tables and fasta files	Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU
Metagenomes - Iberian Margin	Iberian Margin Anaerobic Sediment Metagenomes.
Metagenomic sequences: IODP Site 1244	NCBI accession numbers for metagenomic sequences: IODP Site 1244, Hydrate Ridge, offshore Oregon
metatranscriptomics - upper_lower halocline	Microbial metatranscriptomics: upper and lower halocline water column
Microbe priority experiment counts	Microbe priority experiment counts (OTU counts)
Microbes priority annotations (OTU taxonomy)	Microbes priority annotations (OTU taxonomy)
Microbial 16S rRNA gene amplicon SRA numbers	Microbial 16S rRNA gene amplicon SRA numbers
Microbial community composition of the Cinder Cones Cold Seep	Microbial community composition of the Cinder Cones Cold Seep
Microbial eukaryotic diversity: Axial Seamount SRA	Axial seamount SRA
Microbial eukaryotic diversity: Gorda Ridge SRA	Gorda Ridge SRA
Microbial incubation diversity and geochemistry	Microbial diversity and geochemistry of marine sediment mesocosm, Cape lookout bight, North Carolina
Microsatellite primers for Pollicipes elegans	Microsatellite primer sequences from Pollicipes elegans
Mitochondrial COI barcode sequencing data for Gigantidas childressi veligers, pediveligers, and juveniles	Mitochondrial COI barcode sequencing data for Gigantidas childressi veligers, pediveligers, and juveniles
MtCOI sequence accessions - Pollicipes elegans	Cytochrome oxidase I DNA sequences from Pollicipes elegans
MVCO environmental measurements and high throughput sequencing	Links to high throughput sequencing data and associated MVCO environmental measurements
MVCO Syndiniales amplicon ASV counts	MVCO Syndiniales amplicon ASV counts
Nematostella ocean acidification experiment: Larval heat tolerance	OA experiment: Nematostella larval heat tolerance
Nitrite reductase genes sequence accessions	Nitrite reductase genes sequence accessions
Oyster Cohort Genetics	Database of DNA microsatellite alleles for hatchery-produced oyster cohorts
Oyster Cohort Traits	Performance traits (e.g., survival, growth, size) for hatchery-produced oyster cohorts
Oyster genetic identity and parasite community structure	Oyster genetic identity and parasite community structure
P. xiphias SRA	P. xiphias SRA, accessions, collection info
Palau lakes: invertebrate barcodes	Palau lakes: invertebrate barcodes
Palau lakes: voucher summary	Palau lakes: voucher summary
Peru Margin iTAGs	Fungal iTAG analyses on Peru Margin sediment core samples
planktonic ciliates: DNA accessions	Planktonic ciliate DNA sequence accession numbers at NCBI GenBank
Pleurochrysis carterae virus production	Analysis of temporal dynamics of three virus types (ssDNA PcCV, dsDNA PLV, dsDNA PsEV) persistently co-infecting P. carterae CCMP645
Pocillopora haplotypes at Moorea by site and depth	Pocillopora haplotypes at Moorea by site and depth
Poland_2013: Polyp count by symbiont type summary	Polyp count by symbiont type summary
Poland_2013: Polyp count with multiple symbiont types	Polyp count with multiple symbiont types
Poland_2013: Symbiont types by site and month	Symbiont types by site and month
Pollicipes elegans aggregation genotypes	Genotype data for the three adult barnacle aggregations - Pollicipes elegans
Pollicipes elegans larval genotypes	Larval genotype data for Pollicipes elegans
poly-A mRNA	The eukaryotic (poly-A) metatranscriptome for Canterbury Basin
Polychaete DNA sequences	DNA sequence data deposited on GenBank for polychaetes used in the project studying the evolution and mechanics of burrowing.
Prochlorococcus and Synechococcus nitrite accumulation in batch culture	Prochlorococcus and Synechococcus nitrite accumulation in batch culture
PRS bacteria identification	Culture-independent identification of bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1
Pseudo-nitzschia spp. presence-absence and environmental data
Pxiphias PopStructure mtDNA	Pleuromamma xiphias mitochondrial genetic data (Atlantic; mtDNA) for analyses of population structure across the Atlantic Ocean
qPCR	Quantitative PCR data from sediment samples
qPCR	Quantitative PCR data from sediment samples
qPCR data for archaeal amoA ecotypes	Abundance of ammonia monooxygenase subunit A (amoA) genes determined using TaqMan qPCR.
qPCR data from the Cariaco Meta-Omics Cruises	qPCR data from the CAR212 and CAR216 cruises.
Quantitative PCR data	Quantitative PCR targeting Trichodesmium, UCYN-A, UCYN-B, gamma-24774A11, and Het1, based on the nifH gene.
Raw LC-MS/MS and DNA	Raw LC-MS/MS data, with list of identified peptides, and DNA sequences.
Red Invasive Seaweed - Raw Genotypes	The genotypes from 9 microsatellites generated on individuals of the red invasive seaweed Gracilaria vermiculophylla.
RHB_ostracods	Ostracod species from the Ron Brown cruise - Sargasso Sea
Rockfish microhaplotype sequences	Links to sequence files associated with this project
Ross Sea sequences	Ross Sea sequences link
Salp genome and transcriptome	Antarctic salp genome and RNAseq transcriptome
SBDOM11 mini-remineralization expt.	bacterial abundance, growth rates, and DOC from SBDOM11 cruise
Sciaenid egg identification
SCTLD rapid microbiome characterization	SCTLD microbiome
Seawater data and site descriptions	Site descriptions and physical environmental conditions of reefs where sampling occurred.
SEEPC Bivalve DNA Barcoding Results	Bivalve larvae DNA barcode results
Sequence data accession numbers from mesocosm experiments	Sequence data accession numbers originating from coral and coral mucus experiments.
Single amplified genomes	Single amplified genomes (SAGs)
Single-cell genomics of Chloroflexi	Chloroflexi accessions
Skeletal Organic Matrix Proteins	LC-MS/MS sequenced proteins extracted from Stylophora pistillata skeleton.
South Atlantic Bight nitro cruises 2014	Environmental data, nitrifier abundance, ammonia oxidation rates from the South Atlantic Bight
South Pacific Gyre 16S Amplicons	Accession numbers for raw sequence reads; samples collected on cruise KNOX02RR.
soxB Sequences	soxB gene sequence data from microbial mats at Axial Seamount, 2011.
SPOT virus 18S rDNA peak abund	SPOT Microbial Observatory Protist 18S rDNA TRFLP relative peak abundance
SPOT virus 3H peak abund	SPOT Microbial Observatory Myovirus g23 3' TRFLP relative peak abundance
SPOT virus 5H peak abund	SPOT Microbial Observatory Myovirus g23 5' TRFLP relative peak abundance
SPOT virus ARISA	SPOT Microbial Observatory Bacterial ARISA relative peak abundance
Sulfitobacter phage accessions	Sulfitobacter phage accessions
Symbiont accession numbers	Accession numbers of symbiotic algae in coral
Symbiont type in recovering corals	symbiont type in recovering Porites divaricata corals
T. pseudonana starve-recover experiments: Cell information
T. pseudonana starve-recover experiments: Gene information
T. rotula Common Garden Experiment	T. rotula Common Garden Experiment
T. rotula microbiome global sample	T. rotula microbiome global sample
Temporal genetic patterns in plankton	Temporal genetic patterns in P. xiphias and H. longicornis - Mitochondrial data, station ALOHA
Trematode Parasite COI Sequences	Trematode Parasite COI Sequences
Trichodesmium AHL metatranscriptomes_AE1409	GenBank Trichodesmium accessions and associated metadata
Trichodesmium sequence accessions	GenBank Trichodesmium accessions and associated metadata
V3-V4 16S rRNA sequence accessions from whole larvae and juveniles of Gigantidas childressi and co-located water samples	V3-V4 16S rRNA sequence accessions from whole larvae and juveniles of Gigantidas childressi and co-located water samples
V4 amplicon sequencing of coral tissue	Accession numbers and locations of species analyzed.
V4 SSU rRNA gene primer validation for reef seawater	Partial SSU rRNA genes of bacteria and archaea from reef seawater samples produced using 515F/806R and 515F/806RB primers
Whelan_2014_T3: toxin genes identified in Nemertean species	Toxin genes identified in Nemertean species
Whole community metatranscriptomes	Whole community (3 domain) metatranscriptomes for Peru Margin and Canterbury Basin subsurface sediment core samples
Whole genome sequence data for Pisaster ochraceus
WS1209 strains	Microbial culture collection, strain IDs, locations and depth from cruise WB1209
ZEN 2014 Site Survey Data	Eelgrass 2014 Site Survey Data
Zostera experiment community biomass	Diversity and biomass of eelgrass inhabitants

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Instrument: Thermal Cycler