| 10-cell RNA Sequencing | A procedure that can determine the RNA sequences for all or part of the poly-A tail-containing messenger RNA transcripts in an individual. | PMID:30894605 |
| 16S Ribosomal Gene Sequencing Assay | An amplicon sequencing assay in which universal primers are used to amplify the 16S ribosomal RNA gene from bacterial or archaeal samples for taxonomic identification and profiling. | OBI:0002763 |
| 3' RNA-seq | A method for profiling gene expression in which RNA-sequencing library preparation and sequencing are restricted to a short region at the 3' end of polyadenylated transcripts (typically captured via oligo-dT priming), rather than covering full-length transcripts. | EFO:0010188 |
| 3C | 3C ("chromosome conformation capture") is a molecular technique that measures the physical interaction frequency between genomic loci that are in close spatial proximity within the nucleus. | EFO:0007689 |
| 3C-qPCR | A chromosome conformation capture (3C) method that uses quantitative PCR to measure the interaction frequency between a single pair of genomic loci. | ECO:0000237 |
| 3D ATAC-PALM | A super-resolution imaging technique that combines ATAC-see (a fluorescence-based chromatin accessibility assay) with photoactivated localization microscopy (PALM) to visualize the 3D spatial organization of accessible chromatin in single cells. | Not available |
| 3D Bioprinting | A biofabrication technique that uses layer-by-layer deposition of cells, biomaterials, and growth factors to construct three-dimensional, tissue-like structures. | PMID:26724184 |
| 3D Cell Culture | A cultured cell population grown in a three-dimensional format that more closely mimics the in vivo growth environment than conventional two-dimensional culture. | MSIO:0000159 |
| 4C | 4C (chromosome conformation capture-on-chip) is an extension of 3C that combines chromosome conformation capture with high-throughput sequencing or microarray analysis to identify all genomic loci interacting with a single locus of interest. | EFO:0007690 |
| 5C | 5C ("chromosome conformation capture carbon copy") is an extension of the 3C technique that uses ligation-mediated amplification to study the 3-dimensional organization of multiple genomic loci in parallel. | EFO:0007692 |
| ATAC-Seq | A molecular genetic technique that isolates and sequences chromosomal regions that are rich in open chromatin. First, nuclei are harvested from a cellular sample. Then a hyperactive Tn5 transposase is added to the nuclei where it excises non-nucleosomal DNA strands and ligates co-administered high-throughput sequencing adapters (tagmentation). The tagged DNA fragments are isolated, amplified by PCR and sequenced. The number of reads for specific region of DNA correlate with increased chromatin accessibility and this method can identify regions of transcription factor and nucleosome binding. | NCIT:C156056 |
| ATP Bioluminescence Assay | An analyte assay that detects ATP concentration via light output when luciferase catalyzes the oxidation of luciferin in the presence of ATP, commonly used as a measure of cell viability. | OBI:0002175 |
| Affinity Purification Mass Spectrometry | An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. | pmid:22611051 |
| Allograft | A graft transferred from a donor of one species to a recipient of the same species but different genetic makeup. | NCIT:C60701 |
| Amplicon Sequencing | A DNA sequencing technique that can differentiate cytosine from 5-methylcytosine in a DNA sample. First, a denatured DNA sample is treated with bisulfite which converts non-methylated cytosine to uracil. Next, the sample is amplified using a PCR method that does not discriminate between non-methylated and methylated sequences. The amplified DNA is subjected to nucleotide sequencing. The resulting sequence is compared to an identical control sample of DNA that was not treated with bisulfite. Unmethylated cytosines will be displayed as cytosines in the control sample and as thymines in the bisulfite-treated sample. | EFO:0003747 |
| Angiogenesis Assay | An assay used to measure the formation of new blood vessels from existing vasculature, typically by quantifying endothelial cell tube formation, migration, or sprouting in vitro or in vivo. | Not available |
| Apoptosis Assay | An assay used to detect or quantify cells undergoing apoptosis (programmed cell death), commonly via markers such as caspase activity, Annexin V staining, or DNA fragmentation. | ERO:0001182 |
| Atomic Absorption Spectrophotometry | A technique utilizing a scanning probe to image and analyze the surface of a material with atomic-level resolution. | BAO:0002529 |
| Atomic Absorption Spectroscopy | A spectrometric method that determines the type and concentration of metal elements in a sample, based upon the principle that each elemental metal absorbs a particular wavelength of ultraviolet light when exposed to heat. | NCIT:C85574 |
| Atomic Force Microscopy | A technique utilizing a scanning probe to image and analyze the surface of a material with atomic-level resolution. | NCIT:C17754 |
| Autoradiography | A technique used to locate radioactively labeled molecules, or fragments of molecules, by recording on a photographic or sensor plate the radiation emitted by radioactive material within a molecule. | NCIT:C16314 |
| Barcode-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0008655 |
| Bicinchoninic Acid Assay | A copper-based colorimetric assay for total protein quantification. This assay relies on the formation of a Cu2+-protein complex in a basic environment, followed by reduction of the Cu2+ to Cu+, causing a change of color from green to purple, with a strong absorbance at 562nm. | BAO:0002467 |
| Binding Assay | An assay that measures the interaction or binding affinity between two molecules, such as a ligand and its receptor or an antibody and its antigen. | PMID:21115850 |
| Bio-Layer Interferometry | A label-free optical technique that detects binding interactions by measuring shifts in the interference pattern of light reflected from a layer of immobilized biomolecules on a biosensor tip. | OBI:0002107 |
| Bioluminescence Imaging | An imaging technique that uses fluorescent dye to achieve the desired image. | WIKIDATA:Q4915066 |
| Bisulfite Sequencing | A DNA sequencing technique that can differentiate cytosine from 5-methylcytosine in a DNA sample. First, a denatured DNA sample is treated with bisulfite which converts non-methylated cytosine to uracil. Next, the sample is amplified using a PCR method that does not discriminate between non-methylated and methylated sequences. The amplified DNA is subjected to nucleotide sequencing. The resulting sequence is compared to an identical control sample of DNA that was not treated with bisulfite. Unmethylated cytosines will be displayed as cytosines in the control sample and as thymines in the bisulfite-treated sample. | NCIT:C106054 |
| Brightfield Microscopy | Brightfield microscopy is a type of light microscopy in which objects are seen against a bright background. | NCIT:C19827 |
| Brillouin Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | PMID:29771749 |
| CASFISH | CRISPR/Cas9-mediated fluorescence in situ hybridization, a technique using a catalytically inactive Cas9 (dCas9) fused to a fluorescent tag to visualize specific genomic loci in fixed cells without denaturation. | PMID:26324940 |
| CITE-seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0009294 |
| CLIP-qPCR | A technique combining crosslinking immunoprecipitation (CLIP) of an RNA-binding protein with quantitative PCR to identify and quantify specific bound RNA sequences. | PMID:26721479 |
| CRISPR | A genome-editing and functional-screening technology based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas system, used here as a general assay category for CRISPR-based perturbation experiments. | Not available |
| CUT&RUN | Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a method for mapping DNA-protein interactions using an antibody-targeted nuclease to selectively cleave DNA near a bound protein. | EFO:0009973 |
| CUT&Tag-Sequencing | Cleavage Under Targets and Tagmentation (CUT&Tag), a chromatin profiling method that uses antibody-targeted tagmentation to map the genome-wide location of a protein of interest. | EFO:0920004 |
| Cell Adhesion Assay | Any method to measure the number of dividing cells in a culture, or to measure the change in the proportion of cells that are dividing. | ERO:0001512 |
| Cell Proliferation Assay | Any method to measure the number of dividing cells in a culture, or to measure the change in the proportion of cells that are dividing. | NCIT:C116553 |
| Cell Viability Assay | A colorimetric assay that can assess the viability of cells by quantitation of the reduction of a yellow tetrazolium salt substrate to a product that has a purple color. This assay can measure the cytotoxicity of a chemical or drug by determining the affect of treatment on cell viability. | ERO:000132 |
| Cell-spreading Assay | Any method to measure the number of dividing cells in a culture, or to measure the change in the proportion of cells that are dividing. | PMID:15576905 |
| CellTiter-Glo Luminescent Cell Viability Assay | A colorimetric assay that can assess the viability of cells by quantitation of the reduction of a yellow tetrazolium salt substrate to a product that has a purple color. This assay can measure the cytotoxicity of a chemical or drug by determining the affect of treatment on cell viability. | BAO:0000682 |
| Cerenkov Luminescence Imaging | An imaging modality to study charged particles in tissue by detecting the Cerenkov luminescence produced, allowing the imaging of beta-emitting nuclear medicine probes by optical methods. | NCIT:C151895 |
| ChIA-PET | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with paired end tagged (PET) DNA sequencing to identify the nucleotide sequences for the binding sites occupied by DNA-associated proteins in a sample. | NCIT:C172845 |
| ChIP-PCR | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | ECO:0000227 |
| ChIP-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | NCIT:C106048 |
| ChIP-qPCR assay | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | OBI:0002169 |
| Chemiluminescent Assay | An assay that detects or quantifies an analyte by measuring light emitted from a chemiluminescent reaction. | PMID:28647912 |
| Chemotaxis Assay | An assay that measures the directional movement of cells in response to a chemical gradient (chemoattractant or chemorepellent). | BAO:0010269 |
| Circular Dichroism Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | CHMO:0000323 |
| Co-Immunoprecipitation | Co-immunoprecipitation (Co-IP) is a popular technique for protein interaction discovery. In a co-IP the target antigen precipitated by the antibody "co-precipitates" a binding partner/protein complex from a lysate. It is assumed that these proteins are related to the function of the target antigen at the cellular level. | NCIT:C19830 |
| Co-culture Assay | An assay in which two or more distinct cell types are cultured together to study their interactions. | PMID:4032528 |
| Collision-Induced Dissociation | A method by which fragmentation can be achieved. CID is accomplished by selecting an ion of interest with the mass analyzer and then subjecting that ion to collisions with neutral atoms or molecules. The resulting fragment ions are then mass analyzed. (from The Expanding Role of Mass Spectrometry in Biotechnology by Gary Siuzdak) | NCIT:C48061 |
| Colorimetric Cell Viability Assay | A colorimetric assay that can assess the viability of cells by quantitation of the reduction of a yellow tetrazolium salt substrate to a product that has a purple color. This assay can measure the cytotoxicity of a chemical or drug by determining the affect of treatment on cell viability. | NCIT:C95027 |
| Computational Modeling | The use of statistical analysis, computer analysis, or model organisms to predict outcomes of research. (doegenomes.org) | NCIT:C16461 |
| Computational Tool | A computer program or algorithm used to process, analyze, or interpret biological or experimental data. | mesh:D012984 |
| Computed Tomography | An imaging technique for examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis. | NCIT:C17204 |
| Confocal Microscopy | A system of (usually) epifluorescence light microscopy in which a fine laser beam of light is scanned over the object through the objective lens. This technique is particularly good at rejecting light from outside the plane of focus and so produces higher effective resolution than other microscopy techniques. | NCIT:C17753 |
| Confocal Reflectance Quantitative Phase Microscopy | A system of (usually) epifluorescence light microscopy in which a fine laser beam of light is scanned over the object through the objective lens. This technique is particularly good at rejecting light from outside the plane of focus and so produces higher effective resolution than other microscopy techniques. | mesh:D000097913 |
| Cross-Linking Immunoprecipitation High-throughput Sequencing | A molecular biology method combining crosslinking-immunoprecipitation and high-throughput sequencing techniques to detect and map RNA-protein interactions. In CLIP, whole tissues, organisms or individual cell types are treated with UV irradiation, which introduces covalent bonds between RNA-protein complexes. This is followed by immunoprecipitation and removal of the protein component of the crosslinked complex. The purified RNAs are then fragmented, reduced in size and subjected to high-throughput sequencing for the identification of RNA binding sites. | NCIT:C116152 |
| Cross-Linking Mass Spectrometry | An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. | PRIDE:0000430 |
| Cyclic Immunofluorescence | A method that enables simultaneous detection of multiple biomarkers on a single tissue section using immunofluorescence techniques. | PMID:27925668 |
| Cytochemical Stain | A staining technique used to visualize specific chemical components or structures within cells or tissues under a microscope. | UMLS:C4511272 |
| Cytokine Expression Profile | The identification and quantitation of all of the cytokines expressed in a biological sample. | NCIT:C129886 |
| Cytometric Bead Array Assay | An analyte assay in which a series of beads coated with antibodies, antigens, or other capture molecules are used in combination with flow cytometry to detect multiple analytes simultaneously. | OBI:0000920 |
| Cytotoxicity Assay | An assay that measures the degree to which a substance or treatment is toxic to cells, typically assessed via cell viability, membrane integrity, or metabolic activity. | BAO:0002993 |
| DBiT-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | PMID:33188776 |
| DNA Gene-Expression Microarray | A process that allows thousands of pieces of DNA that are fixed to a glass slide to be analyzed at one time. It is used to identify the genes (pieces of DNA) in specific cells or tissue that are actively used to make RNA, which then may be used to make proteins. | NCIT:C93207 |
| DNA Methylation Array | The use of a high-throughput microarray where all of the known CpG islands either in a single specimen or all of the known promoter sequences of a specimen or a population group are coupled to beads or microwells to determine which are methylated. | NCIT:C165222 |
| DNA Sequencing | The determination of the sequence of purines and pyrimidines in deoxyribonucleic acid (DNA). | NCIT:C153598 |
| DNase-Seq | A molecular genetic technique where genome-wide sequencing is performed on DNA regions that are super sensitive to cleavage by DNase I to identify putative DNA regulatory sequences. | NCIT:C106052 |
| DRIP-seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | Not available |
| Dark Field Microscopy | A microscopic technique in which the light that does not come into contact with the structure or details of interest is subtracted from the ocular image. This yields an image in which the structure or details are alight while the areas where the structures or details are absent are dark. | NCIT:C85837 |
| Deep Mutational Scanning | Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing. | EFO:0010039 |
| Desorption Electrospray Ionization | An ionization method in which charged solvent droplets are sprayed at a sample surface under ambient conditions, desorbing and ionizing surface molecules for direct mass spectrometric analysis. | CHMO:0001660 |
| Dideoxy Chain Termination DNA Sequencing | A DNA sequencing technique in which a mixture of deoxynucleosidetriphosphates (dNTPs) and chain-terminating dNTPs, which are radioactively or fluorescently labeled, are combined within the reaction mixture. Once the reaction is complete, the DNA strands are separated by size, and the labeled chain terminating dNTPs can be read in sequence by the investigator or by a machine. | NCIT:C19641 |
| Differential Interference Contrast Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | BAO:0002511 |
| Differential Scanning Fluorimetry | Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing. | ECO:0006334 |
| Diffusion Weighted Imaging | A type of MRI technique in which diffusion-sensitizing gradients are applied to the imaging sequence. | NCIT:C111116 |
| Direct Long-Read RNA Sequencing | A sequencing method that determines RNA sequence directly from long native RNA molecules without prior conversion to cDNA. | OBI:0002629 |
| Drop-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0008722 |
| Droplet Digital PCR | A type of digital polymerase chain reaction technique in which the sample is fractionated into thousands of tiny droplets using a water-oil emulsion droplet technology, within which individual PCR reactions occur in each droplet. | NCIT:C166064 |
| Dual-Luciferase Reporter Assay | An assay that uses two different luciferase reporter enzymes (typically firefly and Renilla) to simultaneously measure experimental and internal-control reporter gene expression within the same sample. | BAO:0000680 |
| Dye Endocytosis Assay | An assay that measures cellular endocytic activity by quantifying the uptake of a fluorescent or otherwise detectable dye into cells. | Not available |
| Dynamic Contrast-Enhanced Magnetic Resonance Imaging | A type of contrast-enhanced MRI that allows observation of functional properties in addition to structural properties. | NCIT:C62665 |
| Dynamic Force Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | CHMO:0001122 |
| Dynamic Light Scattering | A type of spectroscopy that utilizes a laser beam to irradiate a sample containing particles in suspension, resulting in light scattering. Rapid fluctuations in scattering intensity, around a mean value at a certain angle, occur because of particle diffusion and are dependent upon on particle size. The calculated correlation function yields a diffusion coefficient, for a given temperature and viscosity, which can be used to calculate particle size. | NCIT:C62329 |
| Dynamic Susceptibility Contrast-Enhanced Magnetic Resonance Imaging | A type of magnetic resonance imaging that uses the transient signal reduction induced by the first pass of gadolinium chelate through the brain vessels to calculate cerebral blood flow maps, and to determine the ratio between the cerebral blood volume in the lesion and the cerebral blood volume in normal tissue. | NCIT:C116453 |
| ELISA | A type of enzyme immunoassay in which an antigen or antibody is bound to a solid substrate (e.g., microplate or beads) and interacts with an enzyme-linked antibody or antigen in solution. | NCIT:C16553 |
| Efferocytosis Assay | An assay that measures the phagocytic clearance of apoptotic cells by phagocytes (efferocytosis). | PMID:27815871 |
| Electron Diffraction | Any form of microscopy in which the interactions of electrons with the specimens are used to provide information about the final structure of that specimen. | CHMO:0000142 |
| Electron Microscopy | Any form of microscopy in which the interactions of electrons with the specimens are used to provide information about the final structure of that specimen. | NCIT:C16854 |
| Electron Paramagnetic Resonance Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | ERO:0001093 |
| Electrophoretic Mobility Shift Assay | A molecular biology technique used to detect the interaction of a DNA binding protein with its cognate binding sequence. Labeled DNAs were reacted with crude cell extracts and the complexes are run through a non-denaturing polyacrylamide gel. The migration of the labeled DNA through the gel will be slower by being bound. This shift in electrophoretic mobility indicates functional binding between the protein and the DNA. | NCIT:C19362 |
| Electrospray Ionization Time-of-Flight Mass Spectrometry | An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. | CHMO:0000736 |
| Endotoxin Assay | An assay to detect and quantify endotoxin in a sample. | NCIT:C223372 |
| Energy-Dispersive X-Ray Spectroscopy | A technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. | NCIT:C78869 |
| Enzyme Activity Assay | A procedure performed outside the living body to measure the catalytic activity of an enzyme. | MMO:0000444 |
| Enzyme-Linked Immunospot Assay | A cytometry-based assay in which cells are cultured on a surface coated with a capture antibody for a secreted analyte, which is then detected as discrete spots corresponding to individual secreting cells. | OBI:0600031 |
| Epidemiological Method | Epidemiological methods involve sophisticated statistics and higher mathematics. These methods allow epidemiologists to address issues like non-experimental studies of mechanistic questions in disease etiology, including studies of the impact of the social position of individuals in different social contexts. | NCIT:C16555 |
| FAIRE-Seq | A molecular genetic technique that depletes a biological sample of nucleosomal DNA and then subjects the non-nucleosome-associated DNA to next-generation sequencing. Since nucleosome disruption of chromatin is indicative of active sites of DNA transcription, this technique can isolate DNA sequences that are involved in transcriptional regulation. First, a sample is treated with formaldehyde to form DNA-protein crosslinks, followed by sample lysis and sonication. The processed sample is subjected to phenol/chloroform extraction and the DNA in the aqueous phase is analyzed using next-generation sequencing techniques. | NCIT:C106051 |
| FISH | Any jawed or jawless organisms in the phylum Chordata including the jawless fish, armored fish, cartilaginous fish, ray-finned fish and lobe-finned fish. | NCIT:C17563 |
| Flow Cytometry | A technique for counting, examining or sorting microscopic particles suspended in a stream of fluid. The cells are placed in a fluid (with or without light-sensitive dye) and passed in a stream before a laser or other type of light. | NCIT:C16585 |
| Fluorescence Activated Cell Sorting | Selection and deposition of individual cells of a particular phenotype from a mixed population into a separate tube or tissue culture plate by the use of a fluorescence-activated cell sorter (FACS) and fluorescently-labeled antibodies specific for surface molecules on the cells to be sorted. | NCIT:C17353 |
| Fluorescence Correlation Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | CHMO:0000288 |
| Fluorescence Imaging | An imaging technique that uses fluorescent dye to achieve the desired image. | NCIT:C116489 |
| Fluorescence Lifetime Imaging Microscopy | An imaging technique that produces spatially resolved images based on the differences in the excited state decay rates of fluorescent compounds in a sample. | NCIT:C154786 |
| Fluorescence Microscopy | The use of a special microscope to see objects that give off fluorescent light. For example, cells or tissue can be treated with a substance that contains a fluorescent dye. The dye lights up when viewed under a microscope with a special light. | NCIT:C16856 |
| Fluorescence Recovery After Photo-Bleaching | The use of a special microscope to see objects that give off fluorescent light. For example, cells or tissue can be treated with a substance that contains a fluorescent dye. The dye lights up when viewed under a microscope with a special light. | CHMO:0000065 |
| Fluorescent Antibody Procedure | An immunological procedure in which the antibodies are coupled with molecules which fluoresce under ultra violet (UV) light. This makes them particularly suitable for detection of specific antigens in tissues or on cells. | NCIT:C17370 |
| Fluorescent Cell Barcoding | An immunological procedure in which the antibodies are coupled with molecules which fluoresce under ultra violet (UV) light. This makes them particularly suitable for detection of specific antigens in tissues or on cells. | PMID:33960644 |
| Fluorescent In Situ Sequencing | Use of a DNA or RNA probe to detect the presence of complementary sequences in chromosomes, cells, or tissues. (NCI) | EFO:0008990 |
| Focused Ion Beam Scanning Electron Microscopy | Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing. | FBbi:00050000 |
| Forster Resonance Energy Transfer | A method for determining the distance between two molecules by measuring the energy transfer between two chromophores (a donor and an acceptor) in close proximity. | CHMO:0000062 |
| Fourier Transform Ion Cyclotron Resonance Mass Spectrometry | A type of mass spectrometry that uses the cyclotron frequency of ions in a fixed magnetic field to determine their ionic mass-to-charge ratio. | NCIT:C116571 |
| Fourier-Transform Infrared Spectroscopy | A type of mass spectrometry that uses the cyclotron frequency of ions in a fixed magnetic field to determine their ionic mass-to-charge ratio. | CHMO:0000636 |
| Gas Chromatography Mass Spectrometry | An analytical technique wherein gas chromatography is coupled to mass spectrometry in order to separate, identify, and quantify substances in a sample. | NCIT:C111203 |
| Gelatin Zymography | An SDS-PAGE based procedure used to identify matrix metalloproteinases. | NCIT:C19835 |
| Genotyping | The determination of the nucleotide sequence of the genetic material at a specific locus. | NCIT:C45447 |
| Global Chromatin Profiling | A type of epigenetic modification assay that uses targeted quantitative mass spectrometry to profile post-translational modifications of core histone proteins in chromatin. | OBI:0002961 |
| Global Run-On Sequencing | Global run-on sequencing (GRO-seq), a sequencing-based assay derived from nuclear run-on assays that maps the position and orientation of actively transcribing RNA polymerases genome-wide. | EFO:0005227 |
| Graphite Furnace Atomic Absorption Spectrometry | A technique utilizing a scanning probe to image and analyze the surface of a material with atomic-level resolution. | CHMO:0000239 |
| HL-Chip | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | pmid:32348757 |
| HPLC-MSMS | An analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample. | NCIT:C120691 |
| Hematoxylin and Eosin Staining Method | Hematoxylin-and-eosin, or H&E, is a routine staining procedure of tissue sections. This staining method uses two separate dyes, one staining the nucleus and the other staining the cytoplasm and connective tissue. Hematoxylin is a dark purplish dye that stains the chromatin (nuclear material) within the nucleus. Eosin is an orangish-pink to red dye that stains the cytoplasmic material including connective tissue and collagen. | NCIT:C23011 |
| Hi-C | Hi-C is a method for analyzing the 3-dimensional organization and genome-wide interaction frequencies of chromatin, belonging to the class of chromosome conformation capture techniques. | EFO:0007693 |
| HiChIP | A method that combines chromosome conformation capture, proximity ligation and chromatin immunoprecipitation to isolate DNA from a biospecimen, create a genomic library and analyze 3D chromatin organization. | NCIT:C179435 |
| High Throughput Screening | Use of robots and other automated techniques to screen large numbers of samples. | NCIT:C18472 |
| High-Content Screen | An image analysis technique combining automated fluorescence microscopy with multi-parameter quantitative image analysis for large-scale study of cellular phenotypes. | EFO:0007550 |
| Hydrogels | A three-dimensional network of hydrophilic polymer chains that can absorb and retain large amounts of water, commonly used as a scaffold material in 3D cell culture and tissue engineering. | ENVO:01001562 |
| Hydrophilic Interaction Chromatography | A liquid chromatography technique in which the stationary phase is hydrophilic and the mobile phase is largely organic, separating polar compounds based on their differential partitioning. | CHMO:0002262 |
| Image Cytometry | A flow cytometry technique that utilizes mass spectrometry to detect antibodies labeled with heavy metal ion tags that are bound to antigens of interest on single cells. | mesh:D019044 |
| Imaging | An imaging technique that uses fluorescent dye to achieve the desired image. | NCIT:C17369 |
| Immobilized Metal Affinity Chromatography | A method to purify proteins or peptides from a mixture that leverages their affinity to positively charged ions immobilized on NTA-agarose beads. | NCIT:C161789 |
| ImmunoFISH | A method combining immunolabeling with fluorescent in situ hybridization (FISH) to simultaneously detect the nuclear distribution of a protein and specific DNA or RNA sequences. | EFO:0011016 |
| Immunoassay | An immunological procedure used for the microscopic examination of tissues. It involves the usage of enzyme-antibody or enzyme-antigen conjugates, antienzyme antibodies, or enzyme-antienzyme complexes. | MMO:0000098 |
| Immunocytochemistry | A method for the detection of proteins or antigens on samples of cells that are grown in monolayers or in suspension and deposited on slides, using antibodies or other biomolecules that bind the target and can be visualized through a chemical process. | NCIT:C17731 |
| Immunohistochemistry Staining Method | Immunohistochemical staining techniques allow for the visualization of antigens via the sequential application of a specific antibody to the antigen (primary antibody), a secondary antibody to the primary antibody and an enzyme complex with a chromogenic substrate. The enzymatic activation of the chromogen results in a visible reaction product at the antigen site. The specimen may then be counterstained and coverslipped. Results are interpreted using a light microscope and aid in the differential diagnosis of pathophysiological processes, which may or may not be associated with a particular antigen. | NCIT:C23020 |
| Immunoprecipitation | Antigen aggregation with antibody, in the right ratios, to cause precipitation. (NCI) | NCIT:C16724 |
| In Situ Hybridization | Use of a DNA or RNA probe to detect the presence of complementary sequences in chromosomes, cells, or tissues. (NCI) | NCIT:C17562 |
| In Vitro Cell Killing Assay | A cell killing assay that measures whether, and to what extent, target cells are actively killed by other cells in a cell culture. | OBI:0000903 |
| In Vitro Model | A laboratory model system, such as cultured cells or tissue, used to study biological processes or disease outside of a living organism. | NCIT:C19146 |
| In Vitro Selection | An iterative laboratory process for isolating molecules (e.g., nucleic acids or proteins) with desired properties from a large pool through repeated rounds of selection and amplification outside a living organism. | operation:3795 |
| In Vitro Translation | A cell-free system that synthesizes protein from an RNA or DNA template using cellular translation machinery (ribosomes, tRNAs, and associated factors) extracted from cells. | ERO:0000906 |
| In Vivo Bioluminescence | An imaging technique that detects light emitted by luciferase-expressing cells or tissues within a living organism, used to monitor biological processes such as tumor growth or gene expression over time. | ERO:0000651 |
| In-Cell Western Assay | Any method to measure the number of dividing cells in a culture, or to measure the change in the proportion of cells that are dividing. | BAO:0002423 |
| Inductively-Coupled Plasma Mass Spectrometry | A mass spectrometry technique that uses inductively-coupled plasma generated from argon gas to atomize and ionize a sample. The resulting ions are separated and analyzed using a mass spectrometer. | NCIT:C62328 |
| Interference Reflection Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | CHMO:0002437 |
| Intravital Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | ERO:0001638 |
| Invasion Assay | An in vitro assay, commonly using a reconstituted basement membrane (e.g., Matrigel), that assesses the ability of cells to degrade and migrate through tissue barriers. | NCIT:C16216 |
| Karyotyping | The preparation, analysis, and interpretation of a karyotype, the representation of the chromosome set of a cell. | NCIT:C16768 |
| Knife-Edge Scanning Microscopy | Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing. | PMID:18638197 |
| L1000 mRNA Profiling Assay | A high-throughput gene expression profiling assay in which cultured cells are treated with chemical or genetic perturbations and the transcriptional response of ~1,000 landmark genes is measured, with the remaining transcriptome inferred computationally. | BAO:0010046 |
| Lattice Light Sheet Microscopy | The use of a special microscope to see objects that give off fluorescent light. For example, cells or tissue can be treated with a substance that contains a fluorescent dye. The dye lights up when viewed under a microscope with a special light. | OBI:0003098 |
| Liquid Chromatography Mass Spectrometry | LC/MS is a hyphenated technique, combining the separation power of liquid chromatography (LC), an analytical chromatographic technique for separating ions or molecules dissolved in a solvent, with the detection power of mass spectrometry(MS), a technique to separate gas phase ions according their m/z (mass to charge ratio) value. Used for drug screening, pharmacology studies, environmental analyses and forensics. | NCIT:C18475 |
| Liquid Chromatography/Tandem Mass Spectrometry | An analytical technique wherein liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample. | CHMO:0000701 |
| Low-Vacuum Scanning Electron Microscopy | Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing. | PMID:29546719 |
| Luciferase Reporter Assay | An assay that uses a luciferase reporter gene under the control of a regulatory element of interest to measure gene expression or promoter/enhancer activity via light output. | BAO:0002661 |
| Luminescent Cell Viability Assay | A colorimetric assay that can assess the viability of cells by quantitation of the reduction of a yellow tetrazolium salt substrate to a product that has a purple color. This assay can measure the cytotoxicity of a chemical or drug by determining the affect of treatment on cell viability. | BAO:0000682 |
| MALDI-TOF Mass Spectrometry | An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. | NCIT:C19935 |
| MEMA Cell Growth Assay | Any method to measure the number of dividing cells in a culture, or to measure the change in the proportion of cells that are dividing. | BAO:0010060 |
| MNase-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0003751 |
| MULTI-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0030077 |
| Macrophage Polarization Assay | An assay that measures the differentiation of macrophages into functional phenotypes (e.g., M1 pro-inflammatory or M2 anti-inflammatory) in response to specific stimuli, typically via marker expression or cytokine profiling. | Not available |
| Magnetic Resonance Imaging | Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. | NCIT:C16809 |
| Magnetic Tweezers | A technique that utilizes light waves to exert minute forces as well as transmit energy to isolate and manipulate nanoparticles. | CHMO:0002474 |
| Magnetic Twisting Cytometry | A flow cytometry technique that utilizes mass spectrometry to detect antibodies labeled with heavy metal ion tags that are bound to antigens of interest on single cells. | PMID:11509510 |
| Magnetically Activated Cell Sorting | Selection and deposition of individual cells of a particular phenotype from a mixed population into a separate tube or tissue culture plate by the use of a fluorescence-activated cell sorter (FACS) and fluorescently-labeled antibodies specific for surface molecules on the cells to be sorted. | NCIT:C116641 |
| Mammosphere Formation Assay | An in vitro assay that measures the ability of mammary epithelial or stem/progenitor cells to form free-floating spherical colonies (mammospheres) under non-adherent culture conditions. | PMID:25867607 |
| Mass Cytometry | A flow cytometry technique that utilizes mass spectrometry to detect antibodies labeled with heavy metal ion tags that are bound to antigens of interest on single cells. | NCIT:C187898 |
| Mass Spectrometry | An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. | NCIT:C17156 |
| Mathematical Modeling | The use of statistical analysis, computer analysis, or model organisms to predict outcomes of research. (doegenomes.org) | NCIT:C16870 |
| MeDIP | A DNA methylation profiling assay (methylated DNA immunoprecipitation) that uses an antibody against 5-methylcytosine to enrich for methylated DNA fragments prior to sequencing. | OBI:0000693 |
| MeRIP-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0008803 |
| Methyl Binding Domain Sequencing | An assay in which DNA is enriched using a methyl-binding domain protein to isolate methylated genomic fractions prior to sequencing. | EFO:0003750 |
| Methylation-Specific PCR | Polymerase chain reaction that uses two sets of primers, in two sequential runs of amplification, with the second set intended to amplify a target within the first run product. | PMID:21913069 |
| Micro-computed Tomography | An imaging technique for examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis. | MMO:0000570 |
| MicroRNA Expression Array | A molecular biology device that utilizes a set of defined cDNA clones attached in a specific grid arrangement to a solid support for nucleic acid hybridization assays in gene mapping studies or in determining gene sequences, sequence variations, or gene expression patterns. | OBI:0001335 |
| MicroRNA Sequencing | A next-generation or massively parallel high-throughput DNA sequencing-based procedure that can identify and quantify the microRNA sequences present in a biological sample. | NCIT:C156057 |
| Microcontact Printing | A synthesis method for transferring a molecular pattern onto a substrate surface, typically by coating a patterned stamp with a molecule of interest and bringing it into contact with the surface. | CHMO:0001440 |
| Microfluidics | A technology that manipulates small volumes of fluid (nanoliter to microliter scale) through networks of miniaturized channels, used for high-throughput single-cell or biochemical assays. | mesh:D046210 |
| Micropipette Adhesion Assay | A biophysical assay that uses a micropipette to apply and measure adhesive forces between individual cells or between a cell and a substrate. | PMID:22083316 |
| Micropipette Aspiration | A biophysical technique that uses a fine glass micropipette and controlled suction pressure to measure the mechanical properties (e.g., membrane tension, cortical stiffness) of individual cells. | Not available |
| Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | NCIT:C16853 |
| Migration Assay | An in vitro assay in which cultured cells are monitored and analyzed for their ability to move into an acellular area of a culture material. | NCIT:C19425 |
| Mint-ChIP | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0008813 |
| Modeling | The use of statistical analysis, computer analysis, or model organisms to predict outcomes of research. (doegenomes.org) | NCIT:C16063 |
| Molecular Simulations | The use of computational methods to simulate the physical motions and interactions of atoms or molecules over time. | NCIT:C18097 |
| Monolayer Stress Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | Not available |
| Multi-Angle Light Scattering | A method for determining particle size and molecular weight by measuring the intensity of light scattered from a sample at multiple angles. | CHMO:0000168 |
| Multi-Isotope Mass Spectrometry | An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. | PMID:22246326 |
| Multiparametric Magnetic Resonance Imaging | The combination of multiple magnetic resonance techniques, including diffusion weighted imaging, dynamic contrast-enhanced imaging, and spectroscopy, to achieve an image that will allow for better identification of tumor size and location, as well as possibly identifying cancer spread and aggressiveness. | NCIT:C116458 |
| Multiphoton Microscopy | An imaging technique that uses multiple photons to absorb infrared light, thereby minimizing phototoxicty and photobleaching, making it an ideal method for imaging living specimens, especially those involving deep tissue. | NCIT:C116504 |
| Multiplexed Error-Robust Fluorescence In Situ Hybridization | Use of a DNA or RNA probe to detect the presence of complementary sequences in chromosomes, cells, or tissues. (NCI) | EFO:0008992 |
| Multiplexed Immunofluorescence | A method that enables simultaneous detection of multiple biomarkers on a single tissue section using immunofluorescence techniques. | NCIT:C181928 |
| Multiplexed Immunohistochemistry | A method that enables simultaneous detection of multiple biomarkers on a single tissue section using immunohistochemistry techniques. | NCIT:C181927 |
| Multiplexed Ion Beam Imaging | A method for multiplexed immunohistochemistry that uses secondary ion mass spectrometry to image antibodies tagged with isotopically pure elemental metal reporters. Multiplexed ion beam imaging (MIBI) is capable of analyzing up to 100 targets simultaneously over a five-log dynamic range. This technique enables comprehensive phenotypic profiling and spatial analysis of the tissue microenvironment. | NCIT:C181930 |
| Murine Model | An experimental model that uses mice to study biological processes, disease mechanisms, or the effects of treatments in vivo. | NCIT:C94604 |
| Nano-hmC-Seal | A chemical labeling and capture approach for genome-wide profiling of 5-hydroxymethylcytosine (5hmC) using selective chemical tagging followed by sequencing. | EFO:0010040 |
| NanoString Digital Spatial Profiling | A spatial transcriptomics technique that enables analysis of RNA and protein expression in tissue specimens on slides using multiplexed probe hybridization and digital counting. | EFO:0030029 |
| Nanopatterning | A fabrication technique that creates nanoscale surface features or patterns, used e.g. to control cell adhesion, shape, or substrate mechanics in cell-biology experiments. | Not available |
| Nanopore Sequencing | A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis. | NCIT:C146818 |
| Nanowire | A nanometer-scale wire consisting of metal atoms, silicon or other materials that conduct electricity. Nanowires are one-dimensional, and exhibit unique electrical and optical properties. They are built atom by atom on a solid surface, often as part of a microfluidic device. In addition, they can be coated with molecules such as antibodies that will bind to proteins for both basic science and clinical applications. | NCIT:C62376 |
| Nested PCR | Polymerase chain reaction that uses two sets of primers, in two sequential runs of amplification, with the second set intended to amplify a target within the first run product. | NCIT:C127880 |
| Next Generation Sequencing | Technologies that facilitate the rapid determination of the nucleotide sequence of large numbers of strands or segments of DNA or RNA. | NCIT:C101293 |
| Nm-seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0008828 |
| Not Applicable | Determination of a value is not relevant in the current context. (NCI) | NCIT:C48660 |
| Nuclear Magnetic Resonance | A physical phenomenon involving the interaction of atomic nuclei placed in an external magnetic field with an applied electromagnetic field oscillating at a particular frequency. Magnetic conditions within the material are measured by monitoring the radiation absorbed and emitted by the atomic nuclei. It is the underlying principle of Magnetic Resonance Imaging (MRI). | NCIT:C16921 |
| Optical Coherence Tomography | Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition. (NCI) | NCIT:C20828 |
| Optical Emission Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | CHMO:0000251 |
| Optical Mapping | A technique used for constructing the ordered and high-resolution genome or chromosome sized restriction enzyme map of an organism from a single, stained DNA molecule, digested by the restriction enzyme and imaged by an optical microscope. | NCIT:C116162 |
| Optical Stretcher | A technique that utilizes light waves to exert minute forces as well as transmit energy to isolate and manipulate nanoparticles. | PMID:30404265 |
| Optical Tweezers | A technique that utilizes light waves to exert minute forces as well as transmit energy to isolate and manipulate nanoparticles. | NCIT:C62320 |
| Optogenetic Assay | The combination of genetic and optical methods to control specific cellular events with temporal precision in targeted cells of a functioning biological system. | mesh:D062308 |
| Organoid | A three dimensional mass comprised of a cultured cell or tissue sample that resembles an in vivo tissue or organ. Organoids are grown in vitro from a combination of cells or tissue fragments cultured in medium containing a variety of biochemical factors. | NCIT:C172259 |
| PCR | Polymerase chain reaction that uses two sets of primers, in two sequential runs of amplification, with the second set intended to amplify a target within the first run product. | NCIT:C17003 |
| PET-CT | An imaging technique that combines positron emission tomography and computed tomography acquisition in a single machine to provide co-registered functional and anatomical images. | NCIT:C103512 |
| Paraquat Survival Assay | A survival assay that exposes an organism (commonly Caenorhabditis elegans) to the oxidative-stress-inducing herbicide paraquat to measure resistance to oxidative stress and longevity. | Not available |
| Partial Wave Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | Not available |
| Patient Derived Xenograft | A mouse model for human cancer studies in which a human-derived tumor sample is transplanted into an immunodeficient mouse. | NCIT:C122936 |
| Pending Annotation | A placeholder value indicating that the appropriate assay annotation for this record has not yet been determined or curated. | NCIT:C53470 |
| Permeability Assay | An assay that measures the rate or extent to which a substance passes through a biological or synthetic semi-permeable barrier, such as a cell monolayer or membrane. | BAO:0010083 |
| Phagocytosis Assay | An assay that measures the ability of phagocytic cells to engulf and internalize particles, pathogens, or other cells. | SNOMED:45101000 |
| Photoacoustic Imaging | An imaging technique during which non-ionizing pulses are delivered into tissue and the resulting ultrasonic waves are detected and converted into images. | NCIT:C116749 |
| Photolithography | A synthesis method that uses light to transfer a pattern onto a substrate, typically via a light-sensitive photoresist layer. | CHMO:0001410 |
| Plasmid Construction | The process of assembling or engineering a plasmid vector, typically by inserting a DNA sequence of interest into a plasmid backbone using molecular cloning techniques. | ERO:0001308 |
| PlateSeq | A genome-wide mRNA profiling methodology designed to complement high-throughput screening assays by enabling low-cost, plate-based transcriptomic readouts. | EFO:0008863 |
| Point Accumulation for Imaging in Nanoscale Topography | A super-resolution microscopy technique (PAINT) that achieves nanoscale spatial resolution by imaging the transient, stochastic binding of fluorescently labeled probes to a target structure over time. | FBbi:00000339 |
| Positron Emission Tomography | An imaging technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance. A scanner reveals the tissue location of the metabolically-active substance administered. | NCIT:C17007 |
| Precision Run-On Sequencing | Precision nuclear run-on and sequencing (PRO-seq), a technique that maps the genome-wide position of actively engaged RNA polymerases at nucleotide resolution, including polymerase pause sites. | EFO:0008869 |
| Proteomics Assay | A mass spectrometry assay that identifies and measures proteins in a sample. | OBI:0003781 |
| Proximity Ligation Assay | A technique that leverages immunoassay and DNA amplification technology to detect protein-protein interactions with high specificity and sensitivity. A sample is prepared and then exposed to primary antibodies raised in different species recognizing the target epitopes on the proteins of interest. Then, secondary antibodies that are tagged with short oligonucleotides and that target each primary antibody are added. Next, a mixture comprised of a ligase, PCR components and a connector oligonucleotide, which hybridizes to both oligonucleotide tags and can prime rolling DNA circle synthesis, are added and the sample is subjected to real-time PCR to amplify the DNA circles. Rolling circle synthesis and amplification is only possible if the protein epitopes are in close proximity (i.e. in a protein complex). Finally, a labeled complementary nucleotide probe is added to detect and/or visualize the amplified DNA. | NCIT:C156754 |
| Pull-Down Assay | An in vitro assay used to detect or confirm a physical interaction between two or more proteins (or a protein and another molecule) by using an immobilized bait molecule to capture binding partners from a lysate. | PMID:28667618 |
| QFISH | Quantitative fluorescence in situ hybridization, a technique combining FISH with quantitative fluorescence measurement, commonly used to measure telomere length. | PMID:18228343 |
| Quantitative Multiplex Immunofluorescence | A method that enables simultaneous detection of multiple biomarkers on a single tissue section using immunofluorescence techniques. | EFO:0022989 |
| Quantitative Point Accumulation for Imaging in Nanoscale Topography | A quantitative variant of the PAINT super-resolution microscopy technique that enables counting or quantification of molecules based on transient, stochastic probe-binding events. | PMID:27018580 |
| Questionnaire | A set of questions or items shown to a respondent in order to get answers for research purposes. [PRO Draft Guidance] See also instrument, survey. | NCIT:C17048 |
| RAS Protein Family Activation Assay | An in vitro assay that can indirectly detect the activation of small GTPases in the RAS family through the staining of phosphorylated forms of MEK (MAP2K) family proteins (pMEK). A farnesylated RAS family protein is anchored to an in vitro model of the plasma membrane and, under different conditions, is co-incubated with both a RAF family protein, which binds to and is activated by active RAS proteins, and a MEK family protein, which is phosphorylated by active RAF proteins. pMEK is detected using a donor bead coated with anti-MEK antibodies that is capable of oxidizing an acceptor molecule attached to an anti-pMEK antibody. When the donor and acceptor are in close proximity, the acceptor molecule is oxidized and can be visualized using electron microscopy. | NCIT:C139305 |
| RIP | RNA immunoprecipitation (RIP), a technique used to investigate protein-RNA interactions in the cell by immunoprecipitating an RNA-binding protein along with its bound RNAs. | EFO:0005033 |
| RIP-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0005310 |
| RNA Sequencing | A procedure that can determine the RNA sequences for all or part of the poly-A tail-containing messenger RNA transcripts in an individual. | NCIT:C124261 |
| RNAi Screen | An assay that uses a panel of RNA interference (RNAi) reagents to systematically knock down a large set of genes, one at a time, to identify those involved in a biological process of interest. | FBcv:0003077 |
| RT-PCR | Polymerase chain reaction that uses two sets of primers, in two sequential runs of amplification, with the second set intended to amplify a target within the first run product. | NCIT:C18136 |
| RT-qPCR | Real-time PCR in which an RNA sample is first reverse transcribed into complementary DNA (cDNA) and then quantified by real-time PCR. | MMO:0000462 |
| Raman Spectroscopy | Emission of electromagnetic energy with a shorter frequency (longer wavelength) than that of the incident monochromatic light. Arises from the low probability absorption of quanta with a higher energy than that required for a transition: the difference in energy is emitted as a lower frequency (energy) photon. Allows analysis of vibrational and rotational energy levels using visible incident light. | NCIT:C17157 |
| Reduced Representation Bisulfite Sequencing | A DNA sequencing technique that can differentiate cytosine from 5-methylcytosine in a DNA sample. First, a denatured DNA sample is treated with bisulfite which converts non-methylated cytosine to uracil. Next, the sample is amplified using a PCR method that does not discriminate between non-methylated and methylated sequences. The amplified DNA is subjected to nucleotide sequencing. The resulting sequence is compared to an identical control sample of DNA that was not treated with bisulfite. Unmethylated cytosines will be displayed as cytosines in the control sample and as thymines in the bisulfite-treated sample. | NCIT:C167284 |
| Reverse Phase Protein Array | An antibody-based functional proteomic microarray that can characterize basal protein expression and levels of protein modifications in a series of samples of body fluids or those derived from tissue or cellular lysates. | OBI:0002957 |
| Reverse-Phase High-Performance liquid Chromatography | Liquid chromatography in which the mobile phase is significantly more polar than the nonpolar stationary phase, commonly used to separate small molecules based on hydrophobicity. | CHMO:0001259 |
| Rheometry | The measurement of the flow and deformation behavior of fluids or soft materials in response to applied stress. | CHMO:0000915 |
| Ribo-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0008891 |
| Ribosomal P Protein Antibody Measurement | The determination of the ribosomal P protein antibody present in a sample. | NCIT:C120659 |
| Scanning Angle Interference Microscopy | Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing. | Not available |
| Scanning Electron Microscopy | Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing. | NCIT:C16855 |
| Second-Harmonic Imaging Microscopy | An imaging technique that produces spatially resolved images based on the differences in the excited state decay rates of fluorescent compounds in a sample. | mesh:D000073798 |
| Shotgun Mass Spectrometry | An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced. | PRIDE:0000429 |
| Single Cell ATAC-Seq | A molecular genetic technique where DNA is isolated from single cell (sc) samples and amplified to create a genomic library. Then the library is subjected to ATAC-seq, which isolates and sequences regions rich in open chromatin. | NCIT:C179458 |
| Single Cell Cytokine Detection Chip Assay | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | BAO:0010005 |
| Single Cell DNA Sequencing | The determination of the sequence of purines and pyrimidines in deoxyribonucleic acid (DNA). | NCIT:C223894 |
| Single Cell Gel Electrophoresis | A rapid, simple, visual and sensitive technique for measuring DNA breakage in individual mammalian cells in response to a test agent. A cell is immobilized in agarose and made permeable and the broken DNA migrates out under the influence of the electric field. A damaged cell has the appearance of a comet with a brightly fluorescent cell body and a tail whose length and fluorescence intensity are related to the number of DNA-strand breaks induced by the test agent. | NCIT:C96515 |
| Single Cell RNA-Sequencing | A procedure that determines the nucleotide sequence of RNA transcripts from an amplified sample derived from a single cell, enabling transcriptomic profiling at single-cell resolution. | NCIT:C171152 |
| Single Molecule Forster Resonance Energy Transfer | A single-molecule variant of Forster Resonance Energy Transfer (FRET) that measures the distance-dependent energy transfer between two fluorophores on individual molecules to study conformational dynamics and interactions in real time. | ECO:0008187 |
| Single Nucleotide Polymorphism Array | A genomic microarray-based method able to detect single nucleotide polymorphisms. | NCIT:C116151 |
| Single Nucleus RNA-Sequencing | Single nucleus RNA sequencing examines RNA transcript sequence information from individual nuclei rather than whole cells, using optimized next-generation sequencing technologies, useful for tissues difficult to dissociate into intact single cells. | EFO:0009809 |
| Single-Cell BCR Sequencing | A molecular genetic technique where DNA is isolated from single cell (sc) samples and amplified to create a genomic library. Then the library is subjected to ATAC-seq, which isolates and sequences regions rich in open chromatin. | PMID:31428692 |
| Single-Cell Barcode Chip | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | Not available |
| Single-Cell TCR Sequencing | A molecular genetic technique where DNA is isolated from single cell (sc) samples and amplified to create a genomic library. Then the library is subjected to ATAC-seq, which isolates and sequences regions rich in open chromatin. | PMID:30072991 |
| Single-Molecule Tracking | A microscopy technique that follows the spatial position of individual fluorescently labeled molecules over time to study their movement, diffusion, or interaction dynamics within a cell. | mesh:D000072760 |
| Sirius Red Staining | A histological staining technique that uses Sirius Red dye to selectively stain collagen fibers in tissue sections, commonly used to assess fibrosis. | PMID:25023614 |
| Size Exclusion Chromatography | Gel permeation or sieve chromatography that is performed on porous gels that separate solutes on the basis of size. Smaller solutes are included within the particles of the gel matrix more frequently than larger solutes, thus affecting elution rates. | NCIT:C16433 |
| Small-Angle X-ray Scattering | A technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. | CHMO:0000204 |
| Soft Agar Assay | Soft agar colony formation assay is performed to assay for anchorage independent growth. | NCIT:C16215 |
| Southern Blotting | Electrophoresis-based technique used in genetic testing to detect large deletions in DNA that can be missed by PCR-based genetic testing methods. | NCIT:C16356 |
| Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | NCIT:C17155 |
| Statistical Modeling | The statistical characterization of a system to estimate its future behavior based on past behavior and extrapolation. | NCIT:C16869 |
| Stimulated Emission Depletion Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | PMID:3635273 |
| Stimulated Raman Scattering | Emission of electromagnetic energy with a shorter frequency (longer wavelength) than that of the incident monochromatic light. Arises from the low probability absorption of quanta with a higher energy than that required for a transition: the difference in energy is emitted as a lower frequency (energy) photon. Allows analysis of vibrational and rotational energy levels using visible incident light. | CHMO:0000675 |
| Stochastic Optical Reconstruction Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | FBbi:00000336 |
| Super-Resolution Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | MI:2213 |
| Surface Plasmon Resonance | A quantum optical-electrical phenomena consisting of an alteration in light reflectance as a result of binding of molecules to a surface from which total internal reflection is occurring. Used to detect macromolecular interactions, SPR can be used as the basis for a sensor which is capable of sensitive and quantitative measurement of a broad spectrum of chemical and biological entities. | NCIT:C18117 |
| Surveyor Nuclease Assay | An assay that uses the Surveyor nuclease to detect and cleave DNA at sites of sequence mismatch, commonly used to quantify genome-editing efficiency (e.g., after CRISPR/TALEN treatment). | Not available |
| Synaptophysin Staining Method | This is an immunohistochemical technique utilizing antibody to synaptophysin, an integral membrane glycoprotein present in presynaptic vesicles in neurons. The antibody labels neuroendocrine cells and neurons of the brain, spinal cord and retina. Used to detect neuroendocrine neoplasms including neuroblastomas, ganglioneuroblastomas, ganglioneuromas, pheochromocytomas, chromaffin, and non-chromaffin paragangliomas. | NCIT:C23029 |
| Synthetic Genetic Array | A molecular biology device that utilizes a set of defined cDNA clones attached in a specific grid arrangement to a solid support for nucleic acid hybridization assays in gene mapping studies or in determining gene sequences, sequence variations, or gene expression patterns. | Not available |
| TAB-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | PMID:23196972 |
| TCR Sequencing | A DNA sequencing technique that can differentiate cytosine from 5-methylcytosine in a DNA sample. First, a denatured DNA sample is treated with bisulfite which converts non-methylated cytosine to uracil. Next, the sample is amplified using a PCR method that does not discriminate between non-methylated and methylated sequences. The amplified DNA is subjected to nucleotide sequencing. The resulting sequence is compared to an identical control sample of DNA that was not treated with bisulfite. Unmethylated cytosines will be displayed as cytosines in the control sample and as thymines in the bisulfite-treated sample. | NCIT:C189102 |
| TIRF Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | CHMO:0000094 |
| TRAP Staining | A staining method used to demonstrate the presence of acid phosphatase and tartrate resistant acid phosphatase (TRAP) in osteoclasts. | NCIT:C118401 |
| TUNEL assay | A method to detect apoptosis. | NCIT:C19815 |
| Tandem Mass Spectrometry | Mass spectrometers coupled in series. The targeted compound is selectively ionized, and its characteristic ions are separated from others in the mixture in the first mass spectrometer. The selected primary ions are then decomposed by collision, and from the resulting products the final mass analyzer selects secondary ions characteristic of the targeted compound. Tandem mass spectrometry can achieve specificities and sensitivities equivalent of those of methods such as radioimmunoassay and gas chromatography/mass spectrometry, while performing analyses in much shorter times. | NCIT:C18142 |
| Tandem Mass Tagging | Mass spectrometers coupled in series. The targeted compound is selectively ionized, and its characteristic ions are separated from others in the mixture in the first mass spectrometer. The selected primary ions are then decomposed by collision, and from the resulting products the final mass analyzer selects secondary ions characteristic of the targeted compound. Tandem mass spectrometry can achieve specificities and sensitivities equivalent of those of methods such as radioimmunoassay and gas chromatography/mass spectrometry, while performing analyses in much shorter times. | NCIT:C18142 |
| Target Engagement Assay | An assay type that examines the interaction of ligands with their target biomolecules. | NCIT:C181182 |
| Targeted Genome Sequencing | A DNA sequencing technique in which selected regions of an individual's genome are sequenced. | NCIT:C158253 |
| Targeted Transcriptome Sequencing | An RNA sequencing technique in which selected RNA transcripts of an individual's genome are sequenced. | NCIT:C158252 |
| Thermal Shift Assay | A molecular biology technique used to detect the interaction of a DNA binding protein with its cognate binding sequence. Labeled DNAs were reacted with crude cell extracts and the complexes are run through a non-denaturing polyacrylamide gel. The migration of the labeled DNA through the gel will be slower by being bound. This shift in electrophoretic mobility indicates functional binding between the protein and the DNA. | BAO:0010261 |
| Thin-Layer Chromatography | A planar chromatography technique in which the stationary phase is a thin layer of sorbent applied to a rigid backing (e.g., glass or aluminum), used to separate mixtures of compounds. | CHMO:0001007 |
| Tiling Array | A molecular biology device that utilizes a set of defined cDNA clones attached in a specific grid arrangement to a solid support for nucleic acid hybridization assays in gene mapping studies or in determining gene sequences, sequence variations, or gene expression patterns. | EFO:0002704 |
| Time Lapse Microscopy | The use of various technologies to resolve the structure or features of objects too small or fine to naturally be seen by eye. | CHMO:0001074 |
| Time-Correlated Single Photon Counting | A fluorescence detection technique that measures the relaxation (decay) rate of excited fluorescent molecules by timing individual detected photons relative to an excitation laser pulse. | CHMO:0001963 |
| Tissue Engineering | Application of the principles of bioengineering to combining scaffolds, cells, and biologically active molecules into functional tissues. The goal of tissue engineering is to assemble functional constructs that restore, maintain, or improve damaged tissues or whole organs. | NCIT:C18075 |
| Tissue Microarray | A device for use in high-throughput molecular analysis/screening of clinical tissue specimens. Tissue microarrays spatially arrange 500-1000 tumor biopsies or other tissue onto a microarray block, which is then sliced into sections for probing DNA, RNA or protein targets to provide coincident analysis of all specimens in the array. Subsequent sections can be analyzed with additional probes. | NCIT:C19922 |
| Total Internal Reflection Fluorescence Microscopy | The use of a special microscope to see objects that give off fluorescent light. For example, cells or tissue can be treated with a substance that contains a fluorescent dye. The dye lights up when viewed under a microscope with a special light. | CHMO:0000094 |
| Traction Force Microscopy | A technique utilizing a scanning probe to image and analyze the surface of a material with atomic-level resolution. | Not available |
| Transmission Electron Microscopy | An electron microscopy imaging technique that is utilized to examine structural components of a sample by passing electrons through the specimen. | NCIT:C18216 |
| Transwell Assay | An assay that uses a porous membrane insert (Transwell) to separate two cell compartments, commonly used to measure cell migration, invasion, or barrier permeability. | BAO:0020015 |
| UPLC-MSMS | An analytical technique combining ultra-performance liquid chromatography (UPLC) with tandem mass spectrometry (MS/MS) to separate, identify, and quantify compounds such as metabolites or proteins in complex biological samples. | PMID:20061193 |
| UV Photocrosslinking | A technique that covalently crosslinks nucleic acids to interacting proteins using ultraviolet light, used to capture and study protein-nucleic acid interactions. | MI:0430 |
| Unspecified | Not stated explicitly or in detail. | NCIT:C38046 |
| Vibrational Spectroscopy | The technique of measuring the emission and absorption of different wavelengths (spectra) of visible and non-visible light. This can be done via a spectroscope, which consists of a slit, prism, collimator lens, object lens, and a grating. | CHMO:0000628 |
| Virus Plaque Assay | An assay that is used to determine viral quantity by infecting monolayers of host cells with serially diluted virus, covering the monolayers with an immobilizing overlay after a period of incubation to restrict the spread of the virus to neighboring cells, and counting the resulting visible plaques of infected cells. | NCIT:C174336 |
| Von Kossa Staining | A histochemical staining method that detects calcium deposits (e.g., in bone or calcified tissue) using silver nitrate to precipitate calcium phosphates and carbonates. | SNOMED:117008001 |
| Western Blotting | A method for the detection or identification of proteins or peptides that have been separated by gel electrophoresis and transferred onto nitrocellulose or other type of paper or nylon membrane. The proteins are then detected by reaction with enzymatically labeled or radiolabeled antibody probes. | NCIT:C16357 |
| Whole Exome Sequencing | A procedure that can determine the DNA sequence for all of the exons in an individual. | NCIT:C101295 |
| Whole Genome Bisulfite Sequencing | A procedure that can determine the DNA sequence for nearly the entire genome of an individual. | OBI:0001863 |
| Whole Genome Sequencing | A procedure that can determine the DNA sequence for nearly the entire genome of an individual. | NCIT:C101294 |
| Widefield Fluorescence Microscopy | The use of a special microscope to see objects that give off fluorescent light. For example, cells or tissue can be treated with a substance that contains a fluorescent dye. The dye lights up when viewed under a microscope with a special light. | OBI:0002437 |
| Wound-Healing Assay | A cell-based assay that measures cell motility by creating a 'wound' (gap) in a confluent cell monolayer and capturing the migration of cells to close the gap over time. | ECO:0001099 |
| X-Ray Crystallography | A technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. | NCIT:C17672 |
| X-Ray Diffraction | A technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. | CHMO:0000156 |
| X-Ray Micro-Computed Tomography | An imaging technique for examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis. | PMID:28419369 |
| Xenograft | Cells, tissues, or organs from a donor that are transplanted into a recipient of another species. | NCIT:C12932 |
| cDNA Array | A molecular biology device that utilizes a set of defined cDNA clones attached in a specific grid arrangement to a solid support for nucleic acid hybridization assays in gene mapping studies or in determining gene sequences, sequence variations, or gene expression patterns. | NCIT:C19819 |
| eCLIP-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0009998 |
| mRNA Sequencing | A procedure that can determine the RNA sequences for all or part of the poly-A tail-containing messenger RNA transcripts in an individual. | NCIT:C129432 |
| qPCR | An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction. | NCIT:C51962 |
| scCGI-seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | Not available |
| scNT-Seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | PMID:32868927 |
| scSLAM-seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | PMID:31292545 |
| seqFISH | seqFISH is an in situ multiplexed imaging method that uses sequential rounds of fluorescence in situ hybridization to identify large numbers of RNA species within intact cells. | EFO:0008991 |
| shRNA | An artificial RNA molecule with a tight hairpin turn that can be used to silence target gene expression via RNA interference (RNAi). | NCIT:C123893 |
| siRNA | A 20 to 25-nucleotide double-stranded RNA which is involved in a sequence-specific messenger RNA degradation process known as RNA interference. | NCIT:C2191 |
| smFISH | Single-molecule RNA FISH, a method for detecting and localizing individual RNA molecules within cells using short, fluorescently labeled oligonucleotide probes. | EFO:0009918 |
| smRNA-seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | OBI:0002112 |
| snRNA-seq | A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. | EFO:0009809 |
| Isothermal Titration Calorimetry | The measurement of thermodynamic parameters (e.g. enthalpy) at constant temperature during a titration. | CHMO:0000683 |
| Suspended Microchannel Resonator | Particles are weighed in real-time with the suspended microchannel resonator (SMR) as they flow through a hollow cantilever. In addition to weighing particles with femtogram precision, the SMR can also measure mass density with a resolution of 10-4 g/mL. This is possible since the microchannel resonant frequency is determined by the difference in mass of the particle with respect to that of the displaced fluid. Thus, the particle's density is determined by measuring its mass in two fluids of different densities. The SMR can measure the growth of single cells as well as the absorption of biomolecules to microchannel walls. Scaling the current SMR design by ten-fold will result in a thousand-fold improvement in mass resolution (attogram) and thereby enable single viruses to be weighed with high precision. | PMID:17460669 |
| 10x Multiome | A single-cell multiomic assay that simultaneously profiles gene expression (RNA) and chromatin accessibility (ATAC) from the same individual cell. | EFO:0030059 |
| Visium Spatial Gene Expression | A spatial transcriptomics method developed by 10x Genomics that measures the whole transcriptome or a defined set of transcripts within intact tissue sections while preserving spatial context. | EFO:0010961 |
| Antitumor Drug Screening Assay | A technique used to assess the effectiveness of a potential antineoplastic agent against tumor cells. | NCIT:C15229 |
| Bioelectrochemical Analysis | The use of an electrochemical cell to measure a qualitative or quantitative response of a biological system. | CHMO:0002504 |
| Chimeric Antigen Receptor T-Cell Therapy | Treatment that uses T-cells engineered to express a chimeric antigen receptor (CAR) that specifically targets a particular antigen, most commonly used in cancer immunotherapy. | NCIT:C126102 |
| Cell Cycle Assay | An assay that measures the distribution of cells across different phases of the cell cycle (G0/G1, S, G2/M) to evaluate proliferation status or cell cycle perturbations. | BAO:0002041 |
| Clonality Analysis | A molecular analysis performed to determine whether a population of cells is descended from a single progenitor cell. | NCIT:C63327 |
| Comparative Genomic Hybridization | A technique that detects losses and gains in DNA copy number across an entire genome without the need for cell culturing. | NCIT:C18084 |
| Cryo-Electron Microscopy | Electron microscopy performed on an aqueous sample suspension that is applied as an extremely thin film to a grid and rapidly frozen, preserving its near-native structure for imaging. | NCIT:C18113 |
| Cryo-Electron Tomography | A form of electron tomography in which a cryo-preserved specimen is tilted incrementally in a cryogenic transmission electron microscope to acquire a series of images used to reconstruct its 3D structure. | FBbi:00100015 |
| Data Integration | The process of combining data from multiple sources or of different types into a unified, consistent representation for analysis. | T4FS:0000487 |
| Field-Emission Scanning Electron Microscopy | Scanning electron microscopy that uses a field-emission electron source to produce a finely focused, high-resolution electron beam. | CHMO:0000074 |
| Label-free Protein Quantification by LC/MS | A method for quantitating proteins in samples subjected to liquid chromatography-mass spectrometry (LC/MS) without the use of isotopic or chemical labels. | NCIT:C161825 |
| Metabolite Profiling Assay | An assay that detects and identifies small-molecule chemical entities resulting from biochemical and cellular metabolism. | OBI:0000366 |
| Reporter Gene Assay | An assay that uses a reporter gene (e.g., luciferase, GFP, beta-galactosidase) whose measurable expression serves as a readout of the activity of a promoter, enhancer, or other regulatory element. | BAO:0003006 |
| Single-Molecule Localization Microscopy | A super-resolution fluorescence microscopy technique that localizes individual fluorophore molecules with high precision over many imaging cycles to reconstruct an image beyond the diffraction limit. | Not available |
| Synthesis | The process of producing a chemical compound, usually by the union of simpler chemical compounds. | NCIT:C61408 |
| Targeted Therapy Agent | Any agent that specifically targets or interferes with the synthesis or function of a molecule expressed specifically in or on cells relevant to a disease process, such as a tumor. | NCIT:C163758 |
| Trichrome Staining Method | A histological staining method that uses acid dyes and washes to selectively stain structural elements in tissue samples in three or more contrasting colors, commonly used to visualize collagen and muscle fibers. | NCIT:C23012 |
| Ultrasound Imaging | The use of high-frequency sound waves to generate images of internal body structures. | NCIT:C17230 |
| Transcription profiling by NanoString | A gene expression profiling technique that uses the NanoString nCounter system's multiplexed probe hybridization to capture and digitally count individual mRNA transcripts. | EFO:0030058 |
| Alcian Blue Staining Method | A microscopy staining method that uses Alcian Blue, a cationic copper-containing dye, to detect acidic mucosubstances and glycosaminoglycans in tissue. | NCIT:C92299 |
| Artificial Intelligence | The branch of computer science concerned with creating systems that can perform tasks normally requiring human intelligence, such as learning, reasoning, and problem-solving. | NCIT:C16309 |
| Cell Culture | The maintenance and growth of cells, derived from a strain or cell line, in a controlled laboratory environment outside their original organism. | NCIT:C16396 |
| Clinical Study | Research conducted with human subjects or human-derived material in which an investigator directly interacts with subjects, encompassing clinical trials as well as epidemiologic, behavioral, and health services research. | NCIT:C71104 |
| Cell-free Circulating Tumor DNA Assay | An assay used to detect cell-free circulating tumor DNA in a biological sample, for identification of molecular residual disease and assessment of treatment response. | NCIT:C182622 |
| Co-Immunoprecipitation Mass Spectrometry | A method that combines co-immunoprecipitation (using an antibody to pull down a protein and its binding partners) with mass spectrometry to identify protein-protein interaction partners. | Not available |
| Deep Learning | A subset of machine learning based on artificial neural networks with multiple layers, capable of learning complex representations directly from data. | NCIT:C176258 |
| Gene Ontology Enrichment Analysis | A statistical method that determines whether genes annotated with particular Gene Ontology (GO) terms are significantly over- or under-represented within a gene list of interest, relative to a background set. | EDAM:operation_3501 |
| Gene Set Enrichment Analysis | An inferential statistical data analysis that determines whether an a priori defined set of genes shows statistically significant, concordant differences in expression between two biological states. | OBCS:0000147 |
| Gene Silencing | The process by which the expression of a specific gene is suppressed, occurring naturally (e.g., via RNA interference or DNA methylation) or induced experimentally as a research tool. | NCIT:C39200 |
| Human Induced Pluripotent Stem Cell-derived Cardiomyocytes Culture | The in vitro culture of cardiomyocytes (heart muscle cells) that have been differentiated from human induced pluripotent stem cells (iPSCs), used to model cardiac biology and disease. | Not available |
| Imaging Mass Cytometry | A method that combines laser ablation of tissue specimens with mass spectrometry to image antibodies tagged with isotopically pure metals, enabling highly multiplexed spatial protein detection. | NCIT:C182027 |
| Immunofluorescent Staining Method | A microscopy staining method that uses fluorescently labeled antibodies to detect specific target antigens in preserved cells or tissue. | NCIT:C142337 |
| Immunotherapy | Therapy designed to induce changes in a patient's immune status in order to treat disease, such as cancer. | NCIT:C15262 |
| Viral Transduction | The transfer of genetic material into a cell using a viral vector. | NCIT:C142787 |
| Metastatic Colonization Assay | An in vivo assay that measures the ability of tumor cells to establish and grow secondary colonies at a distant site after introduction into a host organism, modeling the colonization step of metastasis. | Not available |
| Phylogenetic Analysis | The study of evolutionary relationships among organisms or sequences, typically represented as a branching tree (phylogeny) inferred from molecular or morphological data. | NCIT:C18940 |
| Picrosirius Staining | A histochemical staining method using picric acid and Sirius Red dye to selectively stain collagen fibers, commonly used to assess fibrosis and collagen organization in tissue sections. | SNOMED:51567006 |
| Scratch Assay | A cell-based assay, synonymous with the wound-healing assay, in which a 'scratch' is made in a confluent cell monolayer and the subsequent migration of cells to close the gap is measured over time. | ECO:0001099 |
| Structural Variant Analysis | The computational analysis of sequencing or array data to detect large-scale genomic alterations such as deletions, duplications, insertions, inversions, and translocations. | Not available |
| Survival Analysis | A statistical method that analyzes the duration of time until an event of interest occurs, such as death, disease recurrence, or treatment failure. | NCIT:C53372 |
| Targeted Error Correction Sequencing | A targeted sequencing approach that incorporates molecular barcoding or redundant sequencing of the same DNA molecule to computationally distinguish true low-frequency variants from sequencing errors. | Not available |
| Tuba-Seq | Tumor barcoding with ultradeep barcode sequencing | EFO:0008979 |
| SDS-PAGE | A protein assay that allows protein separation by mass in a polyacrylamide-based discontinuous gel. | EFO:0010936 |
| Cell Fractionation | A technique in which sub-cellular components are separated based on their physical properties, such as density in a sucrose density gradient. | MMO:0000679 |
| Multiscale Light Sheet Microscopy | A light-sheet fluorescence microscopy approach that combines imaging at multiple spatial scales (e.g., whole-organism to subcellular) within the same experiment. | OBI:0003098 |
| Light Sheet Microscopy | A fluorescence microscopy technique that captures photons emitted by fluorophores excited with a thin sheet of laser light, illuminating only a thin region of the sample at a time. | OBI:0003098 |
| CODEX | A highly multiplexed cytometric imaging approach that iteratively visualizes many protein targets in a single tissue staining reaction. | NCIT:C181931 |
| in vivo tumor growth | Monitoring of tumor growth (e.g. volume/size over time) in a live animal model, typically as a functional readout rather than a molecular assay. | Not available |
| in silico synthesis | Computational/simulation-based synthesis of a molecule or construct rather than a wet-lab technique. | Not available |
| RNA array | A microarray platform used to measure RNA expression levels. | Not available |
| shRNA-seq | A pooled shRNA screening assay read out by sequencing to identify short hairpin RNA constructs enriched or depleted under a selection condition. | Not available |
| spatial transcriptomics | A general term for assays that measure RNA expression while preserving spatial location information within a tissue section. | Not available |
| in vivo PDX viability | A functional viability readout from a patient-derived xenograft (PDX) model. | Not available |
| histology | Microscopic examination of tissue structure via sectioning and staining. | Not available |
| proximity extension assay | An antibody-based protein detection method (e.g. Olink) in which paired antibodies with attached DNA oligonucleotides bind a target protein, allowing proximity-dependent DNA amplification and readout. | Not available |
| compound screen | A screening assay testing multiple chemical compounds for a biological effect. | Not available |
| metabolic screening | A screening assay assessing metabolic activity or metabolite profiles. | Not available |