Glossary
Every key term, A to Z
The key terms from all the technique guides in one place. A term used by several techniques shows each definition, because the same word can matter differently at different benches.
1,174 terms1,289 definitions
1,174 terms
Numbers and symbols
- 16S rRNA gene
- The small-subunit ribosomal RNA gene of bacteria and archaea; conserved regions anchor primers, variable regions (V1–V9) distinguish taxa.Amplicon & microbiome sequencing
- 28S/18S ratio
- The area of the large ribosomal peak over the small one. Near 2 in intact mammalian total RNA, falling as degradation cuts the longer molecule first. A late, coarse indicator that can also be wrong for non-biological reasons.RNA integrity check
- 2D/3D classification
- Sorting particles by appearance to discard junk and separate conformations.Cryo-EM
- 3′/5′ ratio
- Signal from a 3′-proximal assay divided by signal from a 5′ assay on the same cDNA: a direct readout of degradation and processivity.Reverse transcription
- 3-nt periodicity
- Footprint positions concentrated in one of the three frames along a coding sequence, the signature of translating ribosomes.Specialized RNA sequencing
- 3Rs
- Replacement, reduction and refinement: the framework for humane animal research.Handling & dosing
- 4PL fit
- Four-parameter logistic: bottom, top, midpoint (EC50) and slope. The usual model for ELISA curves.ELISA
- 5' phosphate / 3' OH
- The two groups T4 ligase joins. One partner at each junction must supply the phosphate.Ligation-based cloning
- 5hmC
- 5-hydroxymethylcytosine, an oxidised form of 5mC made by TET enzymes; read as C by bisulfite and EM-seq.Methylation sequencing
- 5-hydroxymethylcytosine (5hmC)
- An oxidation product of 5mC and an intermediate in demethylation. It also resists bisulphite, so standard bisulphite methods report 5mC and 5hmC together.DNA methylation analysis
- 5-methylcytosine (5mC)
- Cytosine methylated at the 5 position, in vertebrates almost entirely at CpG dinucleotides. It base-pairs normally, which is why it has to be converted chemically or captured by affinity before it can be read.DNA methylation analysis
- α-haemolysis
- Partial lysis with oxidation of haemoglobin, a green-brown zone with intact red-cell ghosts.Selective & differential media
- β-haemolysis
- Complete lysis of red cells round a colony, a clear zone seen against the light.Selective & differential media
- β-lactamase
- An enzyme that hydrolyses penicillins such as ampicillin; secreted by cells carrying a bla gene.Selective & differential media
- ΔCp
- The heat-capacity change on unfolding, mostly from hydration of exposed nonpolar groups; it curves the stability against temperature.Differential scanning calorimetry
- ΔF/F₀
- Change in fluorescence divided by the baseline fluorescence; the standard readout of single-wavelength indicators.Calcium imaging
- ΔHvH/ΔHcal
- The calorimetric criterion: about 1 for two-state unfolding, below 1 for multi-domain or intermediate-containing transitions, above 1 for coupled association or a concentration error.Differential scanning calorimetry
- λmax
- The wavelength of maximum emission; for tryptophan about 308–355 nm depending on how exposed and how polar its surroundings are.Intrinsic fluorescence
- σ (reduced molecular weight)
- M(1 − v̄ρ)ω²/RT, the slope of ln c against r²/2 at equilibrium.Analytical ultracentrifugation
- τc
- Rotational correlation time: how long a molecule takes to tumble. It sets the linewidth.NMR spectroscopy
A
- A260 conversion factor
- ng/µL per absorbance unit at 260 nm over a 1 cm path: about 50 for dsDNA, 40 for RNA, 33 for ssDNA. Choosing the wrong one is a silent systematic error of up to a third.DNA quantification & QC
- A260/A230
- The purity ratio that sees guanidine, phenol, polysaccharide and residual salt. Around 2.0–2.2 for a clean prep; well under 1.8 means something an enzyme will notice.Genomic DNA extraction
- The purity ratio that sees guanidinium, phenol and residual salt. Clean RNA sits near 2.0–2.2; well under 1.8 means something is in the tube that reverse transcriptase will notice, even when A260/A280 looks respectable.RNA extraction
- A260/A280 and A260/A230
- Purity ratios for nucleic acids, about 1.8 and 2.0–2.2 for a clean prep. The first catches protein and the second catches chaotropes, phenol and EDTA.UV-Vis spectrophotometry
- Absorbance (A)
- log₁₀ of the ratio of incident to transmitted light. Dimensionless, and defined only relative to the blank the instrument last measured.UV-Vis spectrophotometry
- Absorbed dose (Gy)
- Energy deposited per kilogram of crystal. About 30 MGy is the accepted limit for cryo-cooled protein crystals.X-ray crystallography
- Access (series) resistance
- Resistance between the amplifier and the cell interior, mostly the pipette tip.Patch clamp
- Accessioning
- Registering a sample on arrival, reconciled against the manifest, which is where it acquires the identifier everything afterwards uses.Record keeping & sample tracking
- Acid phenol
- Phenol equilibrated to about pH 4.5. The low pH is what sends DNA into the organic phase and the interphase while RNA stays in the aqueous phase. Buffered phenol at pH 7.9 keeps both nucleic acids aqueous and belongs to DNA work.RNA extraction
- Adapter read-through
- Sequencing past the end of a short insert into the adapter on the far side.Read processing & analysis
- Adjuvant
- A formulation that depots the antigen and activates innate immunity, without which soluble protein is poorly immunogenic.Antibody production
- ADT (antibody-derived tag)
- The DNA barcode on a CITE-seq antibody, counted like a transcript to measure surface protein per cell.Single-cell RNA-seq
- Adventitious carbon
- The hydrocarbon film that adsorbs onto any surface exposed to air, seen as C 1s at about 284.8 eV in XPS.Material characterization
- Affinity maturation
- Somatic hypermutation and selection in germinal centres, which raises affinity over successive boosts.Antibody production
- Affinity tag
- A peptide or protein fused to the target to give it a handle for purification.Affinity purification
- GST, polyhistidine, MBP, FLAG or a biotin acceptor peptide fused to the bait so it can be immobilised reproducibly. Each tag brings its own non-specific binding.Pull-down assays
- Aga2 fusion
- The yeast display format: the fragment fused to Aga2, which disulfide-bonds to Aga1 in the cell wall.Phage & yeast display
- Aggregation onset
- The temperature at which scattering from aggregating protein starts to rise; reported by nanoDSF alongside Tm.Thermal shift assays
- Air–liquid interface ring
- Many organisms build their heaviest biofilm at the meniscus rather than on the bottom, which is why the stain is read as a solution, not through the well.Biofilm assays
- Airy unit (AU)
- The diameter of the focused spot's central disc, 1.22 λ/NA; pinhole sizes are quoted in AU.Confocal microscopy
- Alkaline lysis
- The SDS/NaOH then potassium acetate method that separates plasmid from chromosome by whether the denatured DNA can reanneal on neutralisation.Plasmid preparation
- Allele
- One of the alternative sequences found at a given position. A diploid sample carries two, which may be the same (homozygous) or different (heterozygous).Genotyping
- Allele dropout
- Failure of one allele to reach the readout, from sampling too few molecules or from preferential amplification, which reports a heterozygote as a homozygote.Genotyping
- Allelic discrimination plot
- The two-dimensional scatter of endpoint fluorescence in the two probe channels, in which genotypes appear as clusters rather than as values.Genotyping
- Allelic dropout
- Failure of one allele to amplify, usually because a variant lies under a primer, so a heterozygous site looks homozygous.Exome & targeted panels
- Alpha and beta diversity
- Diversity within one sample (richness, Shannon) and difference between samples (for example Bray–Curtis dissimilarity).Amplicon & microbiome sequencing
- AM ester
- Acetoxymethyl ester form of a dye that crosses membranes and is trapped after esterase cleavage.Calcium imaging
- Ambient RNA
- Free RNA in the suspension, mostly from lysed cells, captured in every droplet along with the cell.Single-cell RNA-seq
- Amplicon
- The product of a PCR: the stretch of DNA between and including the two primers.PCR
- Amplicon carry-over
- Contamination of new reactions with products of earlier PCRs, a common cause of false positives.Contamination control
- Amplicon sequencing
- Reading many copies of a short PCR product over the edited site to get the percentage of alleles carrying each outcome.Base & prime editing
- Amplitude plot
- Fluorescence of every partition, drawn as a cloud of negatives, a cloud of positives, and whatever lies between. The raw data worth looking at before the summary number.Digital PCR
- Anisotropy (r)
- (I∥ − G·I⊥)/(I∥ + 2G·I⊥); it averages linearly over the species in a mixture, weighted by their intensity.Fluorescence polarization
- Annexin V
- A protein that binds PS only in the presence of Ca²⁺; used fluorescently labelled.Apoptosis assays
- Antifade
- Mounting medium that slows photobleaching of fluorophores.Immunofluorescence
- Anti-roll plate
- A glass plate set just above a cryostat knife edge so the section slides out flat instead of curling.Sectioning
- Antisense oligonucleotide (ASO)
- A short synthetic single strand complementary to a target RNA, acting either by recruiting RNase H or by occupying a site on the RNA.Antisense oligonucleotides
- Antisense probe
- An RNA complementary to the target message, made by transcribing from the promoter that faces the insert from the appropriate side. The sense strand cannot hybridise.In vitro transcription
- Apical / basolateral
- The top (lumen-facing) and bottom (tissue-facing) sides of a polarised epithelium, and the matching compartments of an insert.Co-culture
- Apparent molecular weight
- The mass a band reads against the marker, as opposed to the mass calculated from the sequence. The difference between them is often the interesting result.SDS-PAGE
- Apparent permeability (Papp)
- Rate a tracer crosses a barrier per area per donor concentration, in cm/s.Organ-on-chip
- ARMS / allele-specific PCR
- Amplification refractory mutation system: a primer whose 3′-terminal base sits on the variant, so it extends efficiently on one allele and poorly on the other.Genotyping
- Aspect ratio
- Height to width of a feature, or roof span to height of a chamber; extremes collapse or deform.Microfluidic fabrication
- Assay range
- Quoted as mass of DNA in the assay tube (roughly 0.2–120 ng high-sensitivity, 2–1200 ng broad-range), because the limit is the amount of dye available to bind.DNA quantification & QC
- Assay window
- The difference in mP between free and fully bound tracer; it sets the precision of the fraction bound.Fluorescence polarization
- ASV vs OTU
- Exact sequence variants from denoising, versus operational taxonomic units clustered at a fixed identity such as 97%.Amplicon & microbiome sequencing
- A-tailing
- Adding a single 3′ adenine to blunt fragments so they ligate to T-overhang adapters and not to each other.Library construction
- ATR
- Attenuated total reflectance: FTIR sampling by an evanescent wave in a sample pressed onto a crystal.Material characterization
- att site / clonase
- The fixed recombination sites of phage lambda and the enzyme mix that recombines them: attB × attP in a BP reaction, attL × attR in an LR reaction.Seamless assembly
- Audit trail
- The record of who changed what and when. It is most of what distinguishes a tracking system from a spreadsheet.Record keeping & sample tracking
- Autocatalysis
- Acidic degradation products catalysing further ester hydrolysis, especially inside thick parts or in unchanged buffer.Material characterization
- Acceleration of hydrolysis inside a large object by its own trapped acidic degradation products.Release & degradation studies
- Autoclave
- Pressurised steam at 121 °C that kills bacteria, spores and viruses.Buffer & media preparation
- Autofluorescence
- Fluorescence from the tissue or diet itself, such as chlorophyll in chow, that competes with the label.In vivo imaging
- Autofluorescence gate
- The fluorescence threshold taken from an untransfected sample, above which a cell counts as positive.Transfection
- Autoinduction
- Medium formulated so that lactose takes over as the carbon source when glucose runs out, inducing the culture without you adding IPTG.Recombinant expression
- Average size (region)
- The mass-weighted mean length of the part of the trace you select; it is used for the mass-to-molar conversion.Library QC & pooling
- Avidity
- The combined strength of multivalent binding; a polyclonal's apparent affinity is largely avidity, not intrinsic affinity.Antibody production
- The apparent tightening that comes from several weak interactions holding one particle; the particle only releases when every copy does.Phage & yeast display
B
- b and y ions
- The two fragment series produced by cleaving the peptide backbone, holding the N-terminal and C-terminal part respectively. Gaps between consecutive ions are residue masses.Mass spectrometry proteomics
- Backcrossing
- Recombining a winner against an excess of the wild-type gene, then re-selecting, to strip passenger mutations.Directed evolution
- Bait
- The protein fused to the DNA-binding domain, held at the reporter promoter.Yeast two-hybrid
- Bait (probe)
- A biotinylated DNA or RNA oligonucleotide, typically 80–120 nt, complementary to a target region and pulled down with streptavidin beads.Exome & targeted panels
- Bandpass filter
- An optical filter passing a defined band, written as centre/width (485/20 = 475–495 nm). Efficient but fixed, unlike a tunable monochromator.Plate readers & fluorometry
- Barcode rank (knee) plot
- UMIs per barcode against rank; cells form a plateau, empty droplets a lower shoulder, and a sharp knee between them indicates a clean run.Single-cell RNA-seq
- Basal medium
- The defined mixture of salts, glucose, amino acids and vitamins before supplements (DMEM, RPMI 1640, MEM, DMEM/F12).Media & supplements
- Basecalling model
- The neural network that turns raw nanopore signal into bases; fast, high-accuracy and super-accuracy variants trade compute for accuracy.Long-read sequencing
- Baseline
- The flat early cycles the instrument subtracts from each well so that curves start at zero. A badly placed baseline shifts Cq without changing any chemistry.Quantitative PCR (qPCR)
- Basophilic / eosinophilic
- Stained by the basic dye (haematoxylin-like, blue) or by eosin (pink).H&E staining
- Batch effect
- A systematic offset shared by everything processed together. Harmless if both groups are present in every batch; fatal if they are not.Experimental design & controls
- A systematic, gene-specific difference between samples processed at different times. Removable only if it is not aligned with the comparison of interest.Expression microarrays
- Bead region
- A microsphere population identified by its internal dye ratio, carrying one capture antibody. Adjacent regions in the classification space are the ones that spill into each other.Multiplex immunoassays
- Bead-only control
- The same beads and lysate with no antibody. Identifies everything that binds the resin, which is the largest single source of false partners.Immunoprecipitation
- Beer–Lambert law
- A = ε·c·l. Absorbance is proportional to concentration and to path length, and contributions from different species add.UV-Vis spectrophotometry
- Beta / theta
- In array and probe genotyping, the normalised ratio of the two allele signals; clusters are defined in this coordinate rather than in raw intensity.Genotyping
- Beta value
- The array measure of methylation at a CpG: methylated intensity divided by the sum of methylated and unmethylated intensities, plus a small offset. It runs from 0 to 1 and is compressed at both ends, which is why differential testing is often done on the logit-transformed M value instead.DNA methylation analysis
- Methylation level at a CpG: methylated reads ÷ all reads covering it, from 0 to 1.Methylation sequencing
- Bias retardation
- In DIC, the deliberate phase offset between the two sheared beams that sets the background grey level and the relief direction.Brightfield & phase contrast
- Bicarbonate–CO₂ buffer
- The physiological buffer system of most media; its pH is set by the bicarbonate concentration and the CO₂ in the atmosphere.Media & supplements
- Binding capacity
- The mass of DNA a column's resin can hold, roughly 20–30 µg for a mini, 100–120 µg for a midi, 500–600 µg for a maxi. Plasmid beyond it is lost.Plasmid preparation
- Milligrams of tagged protein a millilitre of resin can hold.Affinity purification
- Binning
- Adding neighbouring pixels together on the camera: more signal per pixel, coarser sampling.Widefield fluorescence
- Bioavailability
- The fraction of a dose that reaches the systemic circulation; 100% intravenously, often much less by mouth.Handling & dosing
- Biological indicator
- A vial of Geobacillus stearothermophilus spores placed inside the load and incubated afterwards: the definitive test that a cycle worked, available two days later.Filtration & sterilization
- Biological negative
- Cells lacking one partner (knockdown or knockout), stained with both antibodies. Shows that the spots require the protein, not just the antibody.Proximity ligation assay
- Biological replicate
- An independent sample taken through the whole workflow. The only kind of replicate that supports a statement about biology.Expression microarrays
- An independent sample of the biology (another animal, donor or culture), as opposed to sequencing the same RNA twice.RNA-seq
- Biopanning
- One round of capture on immobilised target, washing, elution and amplification.Phage & yeast display
- Biosafety level (BSL)
- A combination of facility, practices and equipment matched to the risk group of the agent.Lab safety & biosafety
- Biotin-phenol
- The APEX2 substrate. With hydrogen peroxide, the peroxidase turns it into a phenoxyl radical that reacts with electron-rich side chains, mostly tyrosine.Proximity labelling
- Biotin–streptavidin
- The tightest non-covalent pair in common use, with a dissociation constant near 10⁻¹⁴ M. Nothing comes off it by competition, so the elution has to be denaturing or the linker has to be cleavable.Pull-down assays
- Biotinyl-5′-AMP
- The activated biotin that the ligases make. It diffuses a short distance from the enzyme and reacts with nearby lysine amines.Proximity labelling
- BirA*
- The R118G mutant of the E. coli biotin ligase, which releases its reactive intermediate instead of handing it to its one natural substrate. The enzyme behind BioID.Proximity labelling
- Bistability
- Two stable steady states for the same conditions, so the circuit's state depends on its history.Synthetic gene circuits
- Bisulfite conversion
- Chemical deamination of unmethylated cytosine to uracil in single-stranded DNA; 5mC and 5hmC react much more slowly and remain C.Methylation sequencing
- Bisulphite conversion
- Treatment with sodium bisulphite that deaminates unmethylated cytosine to uracil while leaving 5-methylcytosine intact, turning methylation into a C/T sequence difference.DNA methylation analysis
- Blacklist
- A list of genomic regions that give anomalously high signal in nearly every experiment, removed before peak calling.Protein–DNA binding maps
- Blank
- The same buffer and cuvette as the sample, without the analyte. It sets I₀, so a wrong blank is a systematic error on every subsequent reading.UV-Vis spectrophotometry
- Wells with every reagent but no analyte. They measure background, which is subtracted.ELISA
- Sterile medium the photometer is zeroed against, so the medium's own absorbance is not counted as cells.Growth curves
- Bleed-through
- Signal from one dye detected in another dye's channel.Immunofluorescence
- Donor emission detected in the acceptor or FRET channel.FRET, FRAP & FLIM
- Bleed-through (crosstalk)
- Signal from one fluorophore detected in another's channel, usually from the red tail of the emission spectrum.Fluorescent proteins & dyes
- Blinding
- Arranging that the person taking the measurement does not know the group. Most valuable where the readout involves judgement.Experimental design & controls
- Blocked N-terminus
- An N-terminal amine carrying an acetyl, formyl or pyroglutamate group, which cannot couple to PITC; the run gives background only.Edman degradation
- Blocking buffer
- Protein or polymer that covers the membrane's remaining binding capacity. Its composition can compete with the antibody: milk casein with a phospho antibody, milk biotin with streptavidin detection.Western blot
- Blocking oligos
- Adapter-complementary oligos and repeat-rich DNA added to a hybridisation to stop off-target fragments being carried along.Exome & targeted panels
- Bluing
- Converting the red, soluble haematoxylin lake to the blue, insoluble form in a weak alkali.H&E staining
- Blunt end
- A cut straight across both strands, with no overhang. Compatible with any other blunt end, which makes it versatile but inefficient to ligate.Restriction digestion
- Bottom-up (shotgun) proteomics
- Digest the proteins to peptides, identify the peptides, infer the proteins. The default workflow, and the source of the protein inference problem.Mass spectrometry proteomics
- Boyden chamber
- Two compartments separated by a porous membrane, used to measure migration towards an attractant.Migration & invasion
- BQSR
- Base-quality score recalibration: re-estimating base qualities from mismatches at sites not expected to vary.Read processing & analysis
- Bridge balance
- Correction in current clamp for the voltage drop across the pipette.Patch clamp
- Bridging protein
- A third protein in the lysate that binds both bait and prey, producing a pull-down band with no direct contact between them.Pull-down assays
- Brightness
- Extinction coefficient × quantum yield; the photons a fluorophore gives per unit of excitation.Fluorescent proteins & dyes
- Bst polymerase
- The thermostable, strand-displacing polymerase used in LAMP, working around 60–65 °C and starting to denature above about 68 °C.Isothermal amplification
- Bubble products
- Heteroduplexes formed after over-amplification that run anomalously large on a size trace.Library construction
- Bubble trap
- An in-line chamber that catches gas before it reaches the cells.Organ-on-chip
- Budding
- The outgrowth of crypt-like domains from an intestinal organoid, a sign of active stem cells.3D culture & organoids
- Buffer capacity
- How much acid or base a buffer absorbs per unit pH change; highest at pH = pKa and proportional to concentration.Buffer & media preparation
- Buffer capacity (κ)
- Bound calcium added per free calcium added; an indicator adds its own κ to the cell's, blunting transients.Calcium imaging
- Buffer subtraction
- Removing the scattering of solvent and cell by measuring the exact matching buffer under identical conditions.Small-angle X-ray scattering
- Buffer–buffer scan
- A scan with buffer in both cells, run until reproducible, that defines the instrument baseline to subtract.Differential scanning calorimetry
- Buffy coat
- The pale layer of white cells between plasma and red cells in spun blood, often used as a richer starting material for PBMC isolation.Primary cell isolation
- Bulk erosion
- Degradation throughout the material: molecular weight falls everywhere, and mass is lost late and quickly.Material characterization
- Degradation throughout the material at once, because water penetrates faster than chains are cut.Release & degradation studies
- Burden
- The growth cost of expressing a circuit, through competition for the shared translation machinery.Synthetic gene circuits
- Burden limit
- The maximum tumour size allowed before the humane endpoint; commonly 12 mm mean diameter in mice.Disease & implant models
- Burst pressure
- The inlet pressure at which a bonded chip delaminates or leaks; the standard test of a bond.Microfluidic fabrication
- Burst release
- Rapid initial release of payload at or near the carrier surface, before matrix-controlled release begins.Release & degradation studies
- BV/TV and Tb.Th
- Bone volume fraction and trabecular thickness, the standard micro-CT measures of trabecular bone.In vivo imaging
- Bystander edit
- A second C or A inside the window that was edited along with the target, putting extra changes on the same allele.Base & prime editing
C
- C1V1 = C2V2
- Dilution equation: stock concentration × volume taken = final concentration × final volume.Buffer & media preparation
- Caging effect
- Stabilisation of a complex inside the gel matrix, where a dissociated protein is likely to rebind before escaping.EMSA (gel shift)
- Calcein-AM
- A non-fluorescent, membrane-permeant ester that live cells cleave into green calcein and retain.Cell seeding on scaffolds
- Call rate
- The fraction of attempted genotypes that produced a call. Together with concordance on duplicate samples, it is the standard quality metric for a genotyping run.Genotyping
- Calorimetric enthalpy (ΔHcal)
- The area of the transition peak: heat absorbed per mole of protein, independent of any model.Differential scanning calorimetry
- Capacitive transient
- The brief current that charges the membrane at the start of a voltage step.Patch clamp
- Capillary number
- Viscous shear over interfacial tension, μu/γ; the main control on droplet size and break-up regime.Droplet microfluidics
- Capillary scan
- A scan along the capillaries before heating that records each one's fluorescence, used to spot adsorption, aggregation and pipetting errors.Microscale thermophoresis
- Capillary transfer
- Moving DNA from gel to membrane by letting buffer wick through the stack into dry towels; alternatives are vacuum and electroblotting.Southern blot
- Capping efficiency
- The fraction of transcripts that carry a cap. Measured, not assumed, usually by a cleavage assay and mass spectrometry or LC.In vitro transcription
- Carrier
- An inert substance, usually glycogen, added to a dilute sample so the precipitate has something to nucleate on and form a visible pellet.Precipitation
- A large immunogenic protein (KLH, BSA, ovalbumin) coupled to a hapten; it takes most of the antibody response.Antibody production
- Carrier ampholytes
- A mixture of small amphoteric molecules added to the rehydration buffer. They improve protein solubility and smooth the conductivity through the run.2D gel electrophoresis
- Carrier and reductant
- BSA, detergent and DTT in the binding buffer. They block the bead surface, strip weak non-specific binding and keep a cysteine-containing bait from oxidising on the resin.Pull-down assays
- Carry-over
- Liquid brought from one vessel into the next on or in the tip. In a dilution series it always moves material from the stronger tube to the weaker one.Pipetting & serial dilution
- Contamination from the film of supernatant a pellet is wet with, which a single wash at the same force largely removes.Subcellular fractionation
- Liquid from a denser tube carried into the next on a reused tip or pipette, which makes each dilution step smaller than intended.CFU counting
- DNA transferred from one sample to the next on instruments or gloves, which PCR then amplifies.Animal genotyping
- Carry-over inhibition
- RT buffer, residual primer and extraction residues slowing the polymerase. Shows as late Cq values across the plate and is diluted away, not washed away.RT-qPCR
- Catalase
- Enzyme that converts hydrogen peroxide into water and oxygen; detected by bubbling in 3% H₂O₂.Biochemical identification
- Cation-adjusted Mueller–Hinton
- The standard medium for susceptibility testing of non-fastidious bacteria, with defined calcium and magnesium, which affect aminoglycoside and tetracycline activity among others.Antimicrobial susceptibility (MIC)
- CC½
- Correlation between intensities merged from two random halves of the data; used to decide the resolution cutoff.X-ray crystallography
- ccdB counterselection
- A toxic gene between a vector's att sites; cells that take up unreacted vector are killed, so most colonies carry a real product.Seamless assembly
- Cell barcode
- A sequence shared by every primer on one bead (or in one well) that labels all transcripts from that cell.Single-cell RNA-seq
- Cell segmentation
- Drawing the boundary that decides which cell a transcript is counted towards, from nuclei, a fixed expansion, or an imaged cell boundary.Spatial transcriptomics
- CETSA
- Cellular thermal shift assay: thermal stabilisation of a target measured as soluble protein after heating intact cells or lysates.Thermal shift assays
- CFSE
- A fluorescent dye that labels cells covalently, used to tell one population from another (and to follow division).Co-culture
- Chain of custody
- An unbroken, signed and timestamped record of everyone who has held a sample, and under what conditions.Record keeping & sample tracking
- Chance proximity
- Spots from two proteins that are near each other without binding, which rise with their abundance and crowding.Proximity ligation assay
- Chaotropic salt
- A salt such as guanidinium thiocyanate that disrupts ordered water, letting DNA adsorb onto silica. Also a strong enzyme inhibitor, so it must be washed out.Genomic DNA extraction
- A salt such as guanidinium thiocyanate that disrupts ordered water. At molar concentrations it lyses cells and denatures every nuclease at once, which is what protects RNA during the prep, and what has to be washed out afterwards, because it inhibits enzymes just as effectively.RNA extraction
- Chatter
- Regular bands of thick and thin section parallel to the knife edge, caused by vibration of the knife or the block.Sectioning
- Chemical integrator
- A strip placed inside the load whose end point corresponds to a time-at-temperature equivalent, so it reports on the load rather than the chamber.Filtration & sterilization
- Chemical shift (ppm)
- Resonance frequency relative to a reference, in parts per million of the spectrometer frequency; reports the local chemical environment.NMR spectroscopy
- Chemically defined medium
- A medium in which every component and its concentration is known: no serum, hydrolysates or tissue extracts.Media & supplements
- Chemotaxis
- Directed movement up a gradient of a soluble attractant; chemokinesis is a faster but undirected movement.Migration & invasion
- Chimera
- A PCR artefact joining parts of two templates, formed when an incomplete extension primes on another template in a later cycle.Amplicon & microbiome sequencing
- Chimeric spectrum
- A fragment spectrum containing fragments from more than one precursor. The normal case in DIA and commoner in DDA than people assume.Mass spectrometry proteomics
- Chloroform clarification
- Killing the surviving host with a lipid solvent. Effective and cheap, but it destroys lipid-containing phage, so it is not universal.Phage work
- Chromatogram (trace)
- The four fluorescence channels recorded as fragments pass the detector; one peak per base.Sanger sequencing
- Circulating blood volume
- About 7% of body weight in rodents (≈ 72 mL/kg in mice); the basis of every blood-sampling limit.Tissue & blood collection
- Cis/trans ratio
- Share of valid pairs within one chromosome versus between chromosomes; high trans signals random ligation.3D genome mapping
- Class II biosafety cabinet
- Cabinet with HEPA-filtered downflow and front inflow that protects both the work and the operator.Aseptic technique & passaging
- Class II cabinet
- A cabinet protecting operator, sample and environment with HEPA-filtered laminar airflow.Lab safety & biosafety
- Clearance angle
- The small angle (about 3–8°) between the back of the knife bevel and the block face; too small rubs, too large scrapes and chatters.Sectioning
- Cleared lysate
- The supernatant after the neutralised lysate has been chilled and spun hard, or filtered. Loading it before the floc has compacted is what clogs columns.Plasmid preparation
- Clearing
- Replacing ethanol with a solvent miscible with wax, such as xylene; tissue turns translucent.Fixation & processing
- Clearing factor k
- 2.53e11 × ln(rmax/rmin) / rpm²: the hours a 1 S particle needs to cross the tube in that rotor at that speed. A species of s svedbergs clears in k/s hours.Centrifugation
- CLEM
- Correlative light and electron microscopy: imaging the same cell or structure by fluorescence and by EM.TEM & SEM
- CLIP
- Crosslinking and immunoprecipitation: UV-crosslink the RNA to the protein in living cells first, so the complex survives stringent purification.RIP & CLIP
- Cloning efficiency
- The fraction of single cells that grow into a colony; often 10–50% and strongly dependent on medium and cell type.Stable cell line generation
- Cloud-point grafting
- Grafting PEG from a buffer near its precipitation point, so coils shrink and more of them fit on the surface.Surface modification
- Cluster
- A clonal group of copies of one library molecule on the flow cell.Short-read sequencing
- Codebook / Hamming distance
- The barcode scheme used in imaging methods. Spare codewords at a distance of four let a single-round error be corrected and a double error be rejected.Spatial transcriptomics
- Coefficient of variation (CV)
- Standard deviation divided by the mean, as a percentage. The usual way to quote replicate agreement in a plate assay.Pipetting & serial dilution
- Width of the G1 peak divided by its position; the main quality measure of a DNA histogram.Proliferation & cell cycle
- Cold-ischaemia time
- Time between removing the tissue and getting it into fixative; ideally minutes.Fixation & processing
- Collagen proportionate area (CPA)
- Share of a section's area that stains as collagen, used to quantify fibrosis.Special stains
- Collagenase
- A calcium-dependent metalloprotease that cleaves collagen in the extracellular matrix; sold in types with different side activities.Primary cell isolation
- Colloidal gold
- Gold nanoparticles of defined size coupled to protein A or antibodies, visible as dense dots in TEM.TEM & SEM
- Colony PCR
- PCR straight from a colony with primers flanking the insertion site: sizes the junction, but cannot see point mutations.Ligation-based cloning
- Colony-forming unit (CFU)
- Whatever gave rise to one colony: a single cell, or a chain or clump that could not be separated. Plates count CFU, not cells.Plating & streaking
- A cell, chain or clump that gives rise to one colony. CFU/mL is the viable count of a suspension.CFU counting
- Colorimetric LAMP
- Read-out using a pH indicator in a weakly buffered mix: polymerisation releases protons, the pH falls and phenol red turns from pink to yellow.Isothermal amplification
- Compartment marker
- A protein known to be restricted to one organelle, blotted to show where that organelle ended up. The contaminating markers are the controls.Subcellular fractionation
- Compensation
- Mathematical removal of each dye's spillover into other detectors, based on single-stained controls.Flow cytometry & FACS
- Competent cells
- Bacteria in a treated state that lets DNA cross the envelope. The state is fragile: it decays above 0 °C and is largely destroyed by a freeze-thaw cycle.Bacterial transformation
- Complete medium
- Basal medium plus the supplements a line needs, typically serum and glutamine, ready to use.Media & supplements
- Completeness
- Fraction of the unique reflections to a given resolution that were actually measured.X-ray crystallography
- Compression
- Shortening of the section along the cutting direction as the knife pushes the tissue; partly relaxed on a warm water bath.Sectioning
- Concentration polarisation
- The concentrated layer of retained solute that builds against an ultrafiltration membrane under flow, reducing flux and trapping protein.Dialysis & buffer exchange
- Build-up of retained solute at the membrane surface; it limits flux and, if compacted, becomes fouling.Downstream processing
- Condenser aperture diaphragm
- Sets the illumination cone. In brightfield, closing it trades resolution for contrast; in phase contrast it is opened fully so the annulus is not clipped.Brightfield & phase contrast
- Conditional (floxed) allele
- An allele with loxP sites in introns around a critical exon: normal until Cre arrives, null afterwards.Other editing & transgenesis
- Conditioned medium
- Medium taken from one cell type and given to another; a simpler, one-way alternative to co-culture.Co-culture
- Confluence
- The fraction of the growth surface covered by adherent cells, judged under a phase-contrast microscope.Aseptic technique & passaging
- Fraction of the dish surface covered by adherent cells; estimated by eye, not counted.Cell counting & viability
- The percentage of the growth surface covered by cells; most lines are passaged at 70–90% before they pile up or become contact-inhibited.Brightfield & phase contrast
- Conformation-specific secondary
- A secondary antibody that binds native IgG and barely recognises reduced, denatured chains, so the antibody used for capture stays invisible on the blot.Immunoprecipitation
- Confounding
- A nuisance variable that varies with the treatment (day, plate position, operator, reagent lot) so that its effect and the treatment's cannot be separated.Experimental design & controls
- Conjugate
- A ligand attached to the oligo to direct uptake (GalNAc for hepatocytes, a cell-penetrating peptide for a morpholino) which can improve potency by one to two orders of magnitude.Antisense oligonucleotides
- Connector oligonucleotides
- Two short DNA strands that hybridise to both probes at once and are joined by the ligase into a circular template.Proximity ligation assay
- Consensus quality (QV)
- Phred-scaled accuracy of an assembly: Q40 is one error in 10,000 bases, Q50 one in 100,000.Whole-genome sequencing
- Contact angle
- The angle a liquid drop makes with a surface at the three-phase line; lower means more wettable.Surface modification
- Contact inhibition
- The slowing and arrest of division in many adherent lines once cells touch on all sides.Aseptic technique & passaging
- Contact matrix
- Counts of read pairs between every pair of genomic bins; symmetric about the diagonal.3D genome mapping
- Contact time
- How long a disinfectant must stay wet on a surface to work.Lab safety & biosafety
- Contemporaneous record
- An entry written as the work happens rather than reconstructed later. It is what gives dates, volumes and deviations any evidential value.Record keeping & sample tracking
- Contig and N50
- A contig is a continuous assembled sequence; contig N50 is the length at which half the assembly sits in contigs at least that long.Whole-genome sequencing
- Control line
- A line on a lateral-flow strip that develops whatever the result, proving the strip ran and the reagents were active.Biosensors
- Controlled-rate freezing
- Cooling at a defined rate (commonly −1 °C/min), by a programmed freezer or an insulated container.Cryopreservation & banking
- Conversion efficiency
- The fraction of unmethylated cytosines that were actually converted, measured at positions known to be unmethylated. Below about 99% the residual cytosine is read as methylation on every sample in the run.DNA methylation analysis
- Fraction of unmethylated C converted, measured on an unmethylated spike-in such as lambda DNA or on non-CpG cytosines.Methylation sequencing
- Co-precipitation
- Salt or other solutes coming out of solution along with the target and ending up in the pellet.Precipitation
- Copy number
- Plasmid molecules per cell, set by the origin of replication: a few hundred for relaxed-control pUC-type origins, fifteen to twenty for stringent low-copy ones.Plasmid preparation
- Plasmids per cell, set by the origin of replication; multiplies both output and burden.Synthetic gene circuits
- Copy-number reconstruction
- A lane of carrier genomic DNA spiked with a known molar equivalent of the fragment of interest, loaded so band density can be converted into copies per genome.Southern blot
- Costes randomisation
- Comparing a coefficient with values from images whose blocks are scrambled, to test whether overlap exceeds chance.Image analysis
- Co-transfection efficiency
- The fraction of cells receiving both of two plasmids added together; it is high per transfected cell, because uptake is all-or-nothing per cell.Transfection
- Countable range
- The colony numbers per plate (about 30–300 on 90 mm) or per spot (about 3–30 for 10 µL) where counts are both precise and complete.CFU counting
- Counterstain
- A general stain, typically of nuclei, that shows where every cell is so specific labels can be counted per cell.Fluorescent proteins & dyes
- A second stain in a contrasting colour that shows the tissue around the main target.H&E staining
- Coupling enzyme
- The reporting enzyme in a coupled assay, added in large excess so its lag is a few percent of the window and its capacity far above the fastest rate.Enzyme activity assays
- Coverage
- Independent cells carrying each guide, kept up at every passage. 300–500× is a usual target; it decides the sampling noise.CRISPR screens
- Library size divided by the number of clones sampled; at one-fold coverage a sample sees only 63% of the library.Directed evolution
- CpG island
- A few hundred base pairs to a couple of kilobases of unusually CpG-dense, GC-rich sequence, often at a promoter. Island promoters are usually unmethylated in normal tissue, which is why their methylation is informative in cancer.DNA methylation analysis
- A CpG-rich stretch, often at promoters, usually unmethylated in normal tissue; MspI cuts it into short fragments.Methylation sequencing
- CPM / TPM
- Counts per million reads, and transcripts per million, which also divides by transcript length so genes within a sample can be compared.RNA-seq
- Cq (Ct, Cp)
- The fractional cycle at which a well crosses the quantification threshold. A cycle number, not an amount; it becomes an amount only because the reaction doubles.RT-qPCR
- Crabtree effect
- Ethanol formation by aerobic yeast at high glucose uptake rates, even with oxygen in excess.Fermentation
- Cre driver line
- An animal line expressing Cre from a chosen promoter. Its expression pattern, not the floxed allele, decides where and when deletion happens.Other editing & transgenesis
- CRISPRi / CRISPRa
- Dead Cas9 fused to a repressor or an activator: expression is changed, the DNA is not cut.CRISPR screens
- Critical angle
- The incidence angle above which light is totally internally reflected, asin(n₂/n₁), about 64.5° from glass into cytoplasm.Widefield fluorescence
- Critical depth
- The depth at which oxygen consumed by the cells above uses up what diffuses in; cells below it become anoxic.Cell seeding on scaffolds
- Critical micelle concentration (CMC)
- The detergent concentration above which micelles form. Only above the CMC can a detergent solubilise membrane protein, which is why dilution of a lysate can precipitate what it was holding in solution.Cell lysis & protein extraction
- Critical-point drying
- Removing liquid CO₂ above its critical point so no liquid–gas interface crosses the specimen and its surface tension cannot collapse it.TEM & SEM
- Replacing water with liquid CO₂ and taking it past its critical point, so the sample dries with no liquid–gas meniscus.Material characterization
- Cross-hybridisation
- A probe binding a related sequence, typically a paralogue. Produces a confident, reproducible, entirely false change.Expression microarrays
- Crosslink density (ν)
- Elastically effective chains per volume; sets swelling, modulus and mesh size together.Hydrogel synthesis
- Crossover
- A template switch during reassembly of fragments, which is what lets shuffling combine substitutions from different parents.Directed evolution
- Cryoprotectant
- An agent such as DMSO or glycerol that reduces freezing injury; permeating ones enter the cell.Cryopreservation & banking
- A solute (glycerol, DMSO) that reduces ice and salt damage to cells during freezing.Liquid culture & strain storage
- Crystal violet
- A cationic triarylmethane dye used at 0.1%; binds negatively charged surfaces, so it stains cells and matrix without distinguishing them.Biofilm assays
- Crystal violet alternatives
- Safranin and alcian blue stain biomass similarly; resazurin and XTT report metabolic activity; a CFU count after sonication reports viable cells.Biofilm assays
- c(s) distribution
- The distribution of sedimentation coefficients that best fits all velocity scans with the Lamm equation, with diffusion tied to s through f/f0 (Schuck, SEDFIT).Analytical ultracentrifugation
- CTAB
- Cetyltrimethylammonium bromide. In high salt it stays in solution with DNA; drop the salt and the CTAB-DNA complex precipitates, leaving polysaccharides behind.Genomic DNA extraction
- CTF
- Contrast transfer function: how the microscope's defocus and aberrations transfer each spatial frequency into image contrast.Cryo-EM
- Culture adaptation
- Selection of genetic variants (for example 20q11.21 gain, trisomy 12 or 17) that grow better in culture; detected only by karyotyping or copy-number assays.Stem cell culture
- Cumulant analysis
- Fitting the logarithm of the correlogram with a polynomial in lag time; the first term gives the Z-average, the second the PDI (ISO 22412).Dynamic light scattering
- Cut
- A pair of ammonium sulfate concentrations defining a fraction: what stays soluble below the first and precipitates by the second.Precipitation
- c-value
- n times the cell concentration divided by KD. It sets the shape of the isotherm; about 10–100 is the useful window for measuring KD.Isothermal titration calorimetry
- Cytochrome c oxidase
- The terminal respiratory enzyme detected by the oxidase test, present in Pseudomonas, Neisseria and Vibrio but not in Enterobacterales.Biochemical identification
D
- DAB
- 3,3′-Diaminobenzidine, oxidised by HRP into a brown, alcohol-insoluble precipitate.Immunohistochemistry
- Dam / Dcm methylation
- Methylation added by E. coli that blocks some enzymes where it overlaps their site. A property of the host strain the DNA came from.Restriction digestion
- Dam methylation
- Adenine methylation of GATC by the host strain, present in the plasmid you put into the reaction and absent from the product the polymerase makes.Site-directed mutagenesis
- Debye length (κ⁻¹)
- Thickness of the ionic atmosphere around a charged surface: about 3 nm in 10 mM monovalent salt and under 1 nm in physiological buffer.Dynamic light scattering
- Decarboxylase test
- Detects removal of the carboxyl group from lysine, ornithine or arginine; the alkaline products turn the indicator red. Needs low oxygen, hence the oil overlay.Biochemical identification
- Deconvolution
- Estimating the cell-type composition of a multi-cell spot by fitting it against a single-cell reference of the same tissue.Spatial transcriptomics
- De-esterification
- Removal of the AM groups inside the cell, required before the dye binds calcium.Calcium imaging
- Degree of conversion
- The fraction of reactive groups (for example C=C) consumed in a reaction, measured against an unchanging internal standard band.Material characterization
- Degree of methacrylation
- The fraction of gelatin's lysine amines that carry a methacryloyl group, set when GelMA is made.Hydrogel synthesis
- Denaturing gel
- An agarose gel run with formaldehyde, or with the sample denatured by glyoxal, so RNA migrates by length rather than by shape. A native gel can make intact RNA look degraded and cannot be compared between runs.RNA integrity check
- Densitometry
- Integrating band intensity to get a number. Meaningful only inside the blot's linear range, and only after background subtraction.Western blot
- Measuring band intensities from an image, usually as background-subtracted integrated volumes.Gel & blot imaging
- Dephosphorylation
- Removing 5' phosphates with a phosphatase so a singly cut vector cannot be re-sealed by ligase.Restriction digestion
- Depletion
- How much of the target is gone from the supernatant after capture. The cheapest check that the antibody worked, and it needs nothing but a lane.Immunoprecipitation
- Derating
- Reducing a rotor's maximum speed for dense samples or for accumulated stress cycles, as the rotor manual specifies.Centrifugation
- Destabilised reporter
- A reporter fused to a degradation signal (e.g. PEST) so its half-life is short and it follows current promoter activity.Reporter assays
- Destaining
- Dissolving the bound dye in 30% acetic acid (or ethanol) so the absorbance is proportional to the dye rather than to where it sits in the well.Biofilm assays
- Detection floor
- The signal below which a spot cannot be distinguished from background, set by non-specific binding and the detector's fixed read noise.Expression microarrays
- Detection threshold
- The intensity a local maximum must exceed to be counted as a spot. It trades missed dim spots against counted noise.Proximity ligation assay
- The voltage, usually −4 to −6 times the noise σ, that a deflection must cross to be counted as a spike.Extracellular recording
- Detergent-to-protein ratio
- The mass of detergent available per mass of protein and lipid being solubilised. Below roughly 3:1 the extraction is limited by detergent rather than by time.Cell lysis & protein extraction
- DEVD
- The tetrapeptide recognised by caspase-3 and -7, used in fluorogenic and luminogenic substrates.Apoptosis assays
- Deviation
- A recorded difference between what was planned and what was done. Recorded at the time it is information; remembered later it is a story.Record keeping & sample tracking
- Diafiltration
- Exchanging a buffer in a concentrator by repeatedly diluting the retentate with new buffer and re-concentrating. Each cycle divides the permeating solute by the concentration factor.Dialysis & buffer exchange
- Diagnostic digest
- A digest chosen so that the fragment sizes distinguish the construct you want from the ones you might have got.Restriction digestion
- Diastase control (PAS-D)
- A serial section digested with amylase before PAS; glycogen disappears, other PAS-positive material stays.Special stains
- Diavolume
- A volume of new buffer equal to the retentate volume passed through during constant-volume diafiltration.Downstream processing
- Dicer
- The RNase III enzyme that cuts long double-stranded RNA and shRNA hairpins into ~21-nucleotide duplexes. The step a synthetic siRNA skips.RNA interference
- Dideoxynucleotide (ddNTP)
- A nucleotide lacking the 3′ hydroxyl, so the chain cannot be extended past it; dye-labelled in modern chemistry.Sanger sequencing
- Dielectric constant
- How well a solvent screens charge. Alcohol lowers it, which is why water stops solvating the charged phosphate backbone.Precipitation
- Differential centrifugation
- A series of spins of increasing force, each collecting the class of particle that sediments at that force while leaving the slower ones in the supernatant.Subcellular fractionation
- Differential medium
- A medium that makes different organisms look different, usually through a substrate and an indicator or through red blood cells.Selective & differential media
- Differential power (DP)
- The difference in heater power between sample and reference cell needed to keep them at the same temperature; integrated over a peak it gives the heat of one injection.Isothermal titration calorimetry
- Differential scanning fluorimetry (DSF)
- Thermal shift assay with an environment-sensitive dye such as SYPRO Orange, usually run in a qPCR instrument.Thermal shift assays
- Differentiation
- Selective removal of excess dye, here with 0.5–1% hydrochloric acid in 70% ethanol.H&E staining
- Diffraction limit
- The smallest spot an optical system can form; single molecules appear at this size, so resolving them needs a high-numerical-aperture objective.In situ hybridization
- The smallest resolvable distance for a lens, about λ/(2NA) laterally (~200 nm for visible light and a 1.4 NA objective).Super-resolution
- Diffusion interaction parameter (kD)
- Slope of D against concentration, D = D₀(1 + kD·c). Positive for net repulsion, negative for attraction; used in formulation to rank colloidal stability.Dynamic light scattering
- Di-glycine remnant (K-GG)
- The two glycine residues left on a ubiquitinated lysine after trypsin digestion, and the epitope the ubiquitin-site antibodies recognise.Post-translational modification analysis
- Dilution factor
- Every dilution applied before counting, including the dye (1:1 trypan blue = ×2).Cell counting & viability
- How much the tube plated has been diluted from the original: 10⁻⁵ means one part in 100,000. Multiply back by its inverse.CFU counting
- Dilution rate (D)
- Medium flow divided by culture volume; equals μ at chemostat steady state.Fermentation
- DIN
- DNA Integrity Number, 1–10, summarising how much of a sizing trace sits at high molecular weight. The DNA analogue of RIN, the RNA Integrity Number used for RNA on the same instruments.DNA quantification & QC
- Directed differentiation
- Driving pluripotent cells towards one fate with a timed series of growth factors or small molecules that mimic development.Stem cell culture
- Dispersed and continuous phase
- The phase that becomes droplets (usually aqueous) and the phase that carries them (usually a fluorinated oil).Droplet microfluidics
- Dispersion
- The extra-Poisson variability of a gene's counts between biological replicates; its square root is the biological coefficient of variation.RNA-seq
- In a negative-binomial model, the squared biological coefficient of variation of a gene between replicates.Read processing & analysis
- Displacement titration
- Titrating a tight ligand into protein pre-bound to a weaker one, which lowers the apparent affinity into the measurable range.Isothermal titration calorimetry
- Display normalisation
- Dividing the target signal by an epitope-tag signal, so the sort ranks occupancy rather than expression.Phage & yeast display
- Dissolved oxygen (DO)
- Oxygen in the medium, usually given as % of air saturation; controlled at a set point by a cascade.Bioreactor culture
- Division index / proliferation index
- Average divisions per original cell, counting non-dividers or only cells that divided at least once.Proliferation & cell cycle
- Dmax
- The largest distance within the particle, where P(r) falls to zero.Small-angle X-ray scattering
- DMR
- Differentially methylated region: a stretch whose methylation differs between samples, conditions or alleles.Methylation sequencing
- DNase I
- An endonuclease that cuts DNA and not RNA, used to remove genomic DNA from an RNA prep. It needs divalent magnesium, which means it must not be heat-inactivated in place: heating RNA with magnesium in the tube hydrolyses the backbone.RNA extraction
- An enzyme that degrades free DNA released by dead cells, preventing the sticky strands from clumping the suspension.Primary cell isolation
- DO cascade
- The order in which the controller raises oxygen supply: agitation, gas flow, then oxygen fraction in the gas.Bioreactor culture
- The sequence a dissolved-oxygen controller uses: agitation, then gas flow, then oxygen enrichment.Fermentation
- Dome
- A drop of matrix and cells set on a plate and covered with medium; the usual format for organoid culture.3D culture & organoids
- Domestication
- Silently removing internal copies of the assembly enzyme's recognition site from a part, so only the intended ends are cut.Seamless assembly
- Dominant marker
- A resistance gene that works in any strain (kanMX/G418, nat, hph), as opposed to an auxotrophic marker that complements a mutation the strain already carries.Microbial genetics
- Dose (e⁻/Ų)
- Electrons per square ångström delivered to the specimen; 40–60 for a single-particle movie.Cryo-EM
- Double agar overlay
- The standard plaque assay: phage plus host in molten soft agar, poured over a set hard agar base so the lawn and the plaques form in a thin layer.Phage work
- Double normalisation
- Dividing the bleached-region intensity by a reference region, each relative to its pre-bleach level, to correct acquisition bleaching and pool loss.FRET, FRAP & FLIM
- Double referencing
- Subtracting both a reference surface and buffer-only injections to remove bulk effects and drift.SPR & BLI
- Doublet
- Two nuclei that share one barcode in a single-cell experiment; their profile is a mixture.ATAC-seq
- Doublet discrimination
- Removing events made of two cells, which have a longer pulse (larger width) than a single cell with the same total signal.Proliferation & cell cycle
- Double-Z probe pair
- Two half-probes that must hybridise adjacently before an amplification cascade can assemble, so a single mis-bound probe gives no signal.In situ hybridization
- Doubling (generation) time
- Time for the population to double in exponential phase, ln 2 / μ.Growth curves
- Dounce homogeniser
- A glass mortar and a close-fitting glass pestle. The clearance sets the shear, so the same number of strokes means different things in different pestles.Subcellular fractionation
- DpnI
- An enzyme that cuts Dam-methylated DNA, used to destroy the plasmid template a fragment was amplified from.Seamless assembly
- DpnI digestion
- The step that destroys the methylated parental plasmid after amplification, so that what transforms is mostly the new, unmethylated product.Site-directed mutagenesis
- Dripping and jetting
- Break-up at the nozzle, giving uniform droplets, versus break-up of an extended thread downstream, giving a broad distribution.Droplet microfluidics
- Dropout (negative) selection
- Growing the pool for a fortnight so that small fitness differences compound into measurable losses of abundance.CRISPR screens
- Drug loading
- Mass of payload as a percentage of the total particle mass; a different quantity from encapsulation efficiency.Nanoparticle formulation
- Duplicate rate
- The fraction of reads that are PCR copies of another read. High in CLIP by nature, and only interpretable if the library carries UMIs.RIP & CLIP
- Fraction of reads that are copies of a molecule already read; set by library complexity against sequencing depth.Whole-genome sequencing
- Share of reads that are copies of an already-seen molecule; it rises as depth approaches library complexity.Exome & targeted panels
- The share of reads that are copies of a molecule already read; high values mean the library had too few distinct molecules for the depth.RNA-seq
- Duty cycle
- The fraction of a sonication run during which the probe is on. A low duty cycle delivers the same total energy with a much lower peak temperature.Cell lysis & protein extraction
- DV200
- Percentage of RNA fragments longer than 200 nt; the integrity metric used for degraded and FFPE material, where RIN is uninformative.Spatial transcriptomics
- D-value
- Time at a given temperature to reduce a population tenfold. For Geobacillus stearothermophilus spores, D₁₂₁ is about 1.5 min.Filtration & sterilization
- Dye blob
- A broad peak from unincorporated dye terminator left after clean-up, typically near bases 60–90.Sanger sequencing
- Dynamic binding capacity
- Protein a column holds at a given flow rate before breakthrough; always below the static capacity quoted on the datasheet.Chromatography polishing
- Dynamic binding capacity (DBC)
- Product bound per litre of resin when the flow-through reaches a set breakthrough (often 10%) at a given residence time.Downstream processing
- Dynamic range
- The span of concentrations between too few positives to be precise and saturation. Set by partition number and volume, not by the chemistry.Digital PCR
- The span of abundances measurable in one experiment, roughly four orders of magnitude per injection against more than seven in a cell.Mass spectrometry proteomics
- Ratio of a promoter's fully induced to fully repressed output; bounded above by the leak.Synthetic gene circuits
E
- Ear punch
- A 1–2 mm hole punched in the ear; the pattern of holes identifies the animal and the tissue goes to genotyping.Animal genotyping
- ECL
- Enhanced chemiluminescence: HRP oxidises luminol and the light is accumulated on film or a CCD. Sensitive, cheap, and saturating.Western blot
- Enhanced chemiluminescence: light from peroxidase-catalysed oxidation of luminol-based substrates.Gel & blot imaging
- eCLIP
- Enhanced CLIP: no radioactivity, barcoded adapters ligated on the beads, a size-matched input library, and single-nucleotide resolution from read starts.RIP & CLIP
- Edge bead
- The thicker rim of resist at the wafer edge after spinning, which holds the mask off the film unless removed.Microfluidic fabrication
- Edge effect
- The systematic difference between the outer ring of a microplate and its interior, caused mainly by faster evaporation and a temperature gradient.Pipetting & serial dilution
- Systematic difference between the outer ring of wells and the interior, caused by evaporation and temperature gradients.Plate readers & fluorometry
- Different evaporation and temperature in the outer wells of a plate, which shifts their readings.Viability & cytotoxicity
- Systematically different readings from the outer ring of a microplate, from evaporation and thermal gradients. Avoided by filling the outer wells with medium.Biofilm assays
- Outer wells of a plate evaporate and warm differently, so cells there grow differently and read differently.Live-cell & time-lapse
- Editing window
- The few protospacer positions a tethered deaminase can reach, typically around positions 4–8 from the PAM-distal end. It is a property of the editor, not something you aim.Base & prime editing
- Effector : target ratio
- The number of killer cells per target cell in a cytotoxicity assay.Co-culture
- Efficiency of plating (EOP)
- Plaques formed on a test host divided by plaques formed on a reference host from the same stock, a measure of host range as much as of technique.Phage work
- Efficiency-corrected ratio
- Replacing the 2 in 2^−ΔΔCq with each assay's measured (1 + E). Needed when target and reference efficiencies differ, and harmless when they do not.RT-qPCR
- Egg-box junction
- Calcium ions held between paired guluronate blocks of two alginate chains.Hydrogel synthesis
- Electropherogram
- The trace of fluorescence against migration time from a capillary or chip separation, plotted against size once the sizing ladder has calibrated the time axis. It is the primary data; the ratio and the score are summaries of it.RNA integrity check
- Electrophoretic mobility
- Particle velocity per unit field strength, measured by electrophoretic light scattering and converted to a zeta potential.Dynamic light scattering
- ELN
- Electronic lab notebook: a versioned, timestamped, searchable record with an audit trail of edits and attached raw data.Record keeping & sample tracking
- Embryoid body
- A floating aggregate of pluripotent cells that differentiates spontaneously into cells of all three germ layers; used to test pluripotency.Stem cell culture
- Emission filter
- A filter in front of the camera that passes the stain's fluorescence and blocks the excitation light.Gel & blot imaging
- Encapsulation efficiency
- Fraction of the offered payload that ends up inside the particles, measured after the free payload is separated.Nanoparticle formulation
- Endosomal escape
- The step at which an internalised complex breaks out of the endosome; usually the limiting step for chemical transfection.Transfection
- Endotoxin unit (EU)
- The activity measure for lipopolysaccharide, assayed by LAL. Standard preps run at tens to hundreds of EU/µg; endotoxin-free preps are below 0.1.Plasmid preparation
- Endpoint read
- Every partition is read once, after cycling, as positive or negative. There is no real-time curve and no Cq.Digital PCR
- Endpoint titre
- The highest dilution of a serum or supernatant that still gives a defined signal above background in an immunoassay.Antibody production
- Engineering stress and strain
- Force over original area, and change in length over original length.Tensile & compression testing
- Enrichment factor
- The share of a marker found in a fraction divided by the share of the total protein in that fraction. It is the number a marker blot actually supports, and 1.0 means the fraction is no better than the homogenate.Subcellular fractionation
- How much more often an improved clone survives a round than the background; the number that decides how many rounds are needed.Directed evolution
- Enrichment specificity
- The fraction of identified peptides in the enriched sample that actually carry the modification. Below about 60% most of the instrument time went on unmodified peptides.Post-translational modification analysis
- Entanglement concentration
- The polymer concentration above which chains overlap and entangle enough to hold a jet together as a fibre.Scaffold fabrication
- Enthalpy–entropy compensation
- The common observation that changes in ΔH between related ligands are partly offset by changes in −TΔS, leaving ΔG similar.Isothermal titration calorimetry
- Epistasis
- Dependence of a substitution's effect on the rest of the sequence; diminishing-returns epistasis is why later generations deliver less.Directed evolution
- Equimolar mix
- Equal numbers of molecules of every piece, which is not the same as equal masses.Seamless assembly
- Equimolar pool
- A pool in which each library contributes the same number of molecules, so each gets a similar number of reads.Library QC & pooling
- Essential agreement
- Two MIC methods agree essentially when their results are within one two-fold dilution of each other.Antimicrobial susceptibility (MIC)
- ETD and EThcD
- Electron-transfer fragmentation, alone or with supplemental collisional activation, which cleaves the backbone while leaving labile modifications attached.Post-translational modification analysis
- Ethidium homodimer-1 (EthD-1)
- A red DNA dye excluded by intact membranes, so it marks dead or damaged cells.Cell seeding on scaffolds
- Evanescent field
- The exponentially decaying light beyond a totally reflecting surface that excites only the first ~100 nm in TIRF.Widefield fluorescence
- Excess heat capacity
- The heat capacity of the protein above its native baseline, in kJ/mol/K, after subtracting the buffer scan and dividing by moles of protein.Differential scanning calorimetry
- Exo probe
- The RPA-specific fluorescent probe, cleaved by an exonuclease only when hybridised to the amplicon, which makes a real-time RPA read sequence-specific.Isothermal amplification
- Expansion factor
- The ratio of gel size after and before expansion (~4× for proExM); resolution improves by the same factor.Super-resolution
- Experimental unit
- The smallest thing that could independently have received a different treatment. It is what n counts, and it is often a flask, a cage or an animal rather than a well.Experimental design & controls
- Explant
- A small piece of tissue placed in culture so that cells grow out of it onto the dish.Primary cell isolation
- Exponential feeding
- Increasing the feed rate exponentially so that the culture grows at a chosen, constant μ.Fermentation
- Exponential (log) phase
- Growth at a constant specific rate, a straight line of ln(OD) against time.Growth curves
- Extended direct transfer
- A MALDI spotting method in which the smear is overlaid with 70% formic acid before matrix, to release proteins from thick-walled cells.Biochemical identification
- External probe
- A probe lying outside the sequence that was introduced, so it detects only the endogenous locus. It is the standard way to prove a targeted insertion is where it should be, since a randomly integrated construct carries no probe sequence.Southern blot
- Extinction coefficient
- The absorbance of a protein at a defined concentration and path length, calculable from its tryptophan, tyrosine and cystine content. Often quoted as the A280 of a 1 mg/mL solution in a 1 cm path.Protein quantification
- Extinction coefficient (ε)
- How strongly one species absorbs at one wavelength. Quoted molar (M⁻¹cm⁻¹) or as a specific absorbance for 1 mg/mL or 1% solutions.UV-Vis spectrophotometry
- Extrusion
- Repeated passage through a polycarbonate membrane to bring vesicles to a defined size.Nanoparticle formulation
F
- F₀
- Accumulated lethality of a moist-heat cycle, in equivalent minutes at 121.1 °C with z = 10 °C. The reference cycle, 121 °C for 15 min at the load, is F₀ = 15.Filtration & sterilization
- Far-UV CD
- The 180–250 nm region, dominated by the peptide backbone; reports secondary structure.Circular dichroism
- Fast region
- The inter-peak stretch where early degradation products appear. Watching it is how you catch degradation before the bands look wrong.RNA integrity check
- FASTQ
- Text format holding each read's sequence and per-base quality scores.Short-read sequencing
- FDR (adjusted p)
- The expected share of false positives among the genes called; 5% is the usual threshold.RNA-seq
- Fed-batch
- A culture started in batch and then fed concentrated nutrients without removing medium, to extend growth and production.Bioreactor culture
- FEP tube
- A fluorinated polymer tube with a refractive index close to water, used to hold live samples in the light path.Light-sheet microscopy
- Fibre volley
- The small, early deflection from the stimulated axons themselves, which reports how many fibres were recruited.Extracellular recording
- Ficoll-Paque
- A density medium of sucrose polymer and sodium diatrizoate at 1.077 g/mL, used to separate mononuclear cells from blood.Primary cell isolation
- Fidelity
- How rarely the polymerase inserts a wrong base. Proofreading enzymes are roughly 50–300× more accurate than Taq.PCR
- Fiducial frame
- Printed markers around the capture area used to align the brightfield image to the barcode coordinates. Without the alignment there are no coordinates.Spatial transcriptomics
- Fiducial markers
- Bright, stable beads used to measure and correct stage drift over long localisation acquisitions.Super-resolution
- Field EPSP (fEPSP)
- The extracellular reflection of synchronous excitatory synaptic currents; its initial slope measures synaptic strength.Extracellular recording
- Field (site)
- One camera image within a well; a well is usually sampled with several fields.Live-cell & time-lapse
- Film saturation
- The flattening of film response near maximum density, which compresses every intensity ratio measured from a long exposure.Northern blot
- Filter cube
- Excitation filter, dichroic mirror and emission filter matched to one fluorophore.Widefield fluorescence
- First-derivative Tm
- Tm taken as the temperature of the steepest rise of the melting curve, the standard analysis for DSF and nanoDSF.Thermal shift assays
- Flat-field correction
- Dividing an image by the illumination profile so equal objects give equal intensities across the field.Image analysis
- FLNC read
- Full-length non-chimeric: a consensus read with both cDNA primers and a poly(A) tail, and no internal primer.Specialized RNA sequencing
- Flory–Rehner equation
- Balances mixing and elastic free energy to give equilibrium swelling from crosslink density and the polymer–solvent χ parameter.Hydrogel synthesis
- Flow focusing
- A geometry where the continuous phase enters from both sides and squeezes the dispersed stream through a narrow nozzle.Droplet microfluidics
- Flow-rate ratio
- Aqueous to organic volumetric ratio in a micromixer; higher ratios mix faster and leave less residual solvent.Nanoparticle formulation
- Flow-through
- What passes the column without binding.Affinity purification
- Flow-through mode
- Running a column at conditions where the contaminants bind and the product does not: fast, high capacity, and often overlooked.Chromatography polishing
- Chromatography in which the product passes and impurities bind.Downstream processing
- Fluorescence lifetime
- The average time a fluorophore stays excited before emitting, a few nanoseconds for fluorescent proteins; FRET shortens the donor's.FRET, FRAP & FLIM
- Fluorosurfactant
- A PEG–perfluoropolyether block surfactant that stabilises water-in-fluorinated-oil droplets and is biocompatible.Droplet microfluidics
- FMO control
- All stains minus one; defines the boundary between negative and positive for that marker.Flow cytometry & FACS
- Fnorm
- Normalised fluorescence: hot-region fluorescence divided by the initial cold fluorescence, in parts per thousand.Microscale thermophoresis
- FokI dimer
- The nuclease domain used by TALENs and ZFNs. Only active as a dimer, so cutting requires two monomers bound the right distance apart.Other editing & transgenesis
- Fold change over control
- The ratio of a protein's signal in the fusion sample to its signal in the enzyme-alone control. The only number that defines a neighbour.Proximity labelling
- Fold induction
- Normalised signal of the treated condition divided by that of the untreated one.Reporter assays
- Fold-80 base penalty
- Mean target depth divided by the depth reached by 80% of target bases; a measure of capture evenness.Exome & targeted panels
- Footprint
- The ~28–30 nt piece of mRNA protected from nuclease by a ribosome.Specialized RNA sequencing
- A small dip in insertions where a bound transcription factor protects its motif from Tn5.ATAC-seq
- Foreign-body response
- The inflammatory and fibrotic reaction to an implant, ending in a collagen capsule around it.Disease & implant models
- Formaldehyde gel
- The standard denaturing system: formaldehyde in the gel and the sample buffer, run in MOPS, which keeps RNA extended so mobility tracks length.Northern blot
- Förster radius (R0)
- Donor–acceptor distance at which FRET efficiency is 50%; set by spectral overlap, donor quantum yield, orientation (κ²) and refractive index.FRET, FRAP & FLIM
- Four-parameter logistic
- Sigmoid with top, bottom, midpoint and Hill slope, fitted to response against log dose.Viability & cytotoxicity
- Frame interval
- Time between consecutive time points; it limits how precisely events can be timed and cells tracked.Live-cell & time-lapse
- Free-floating section
- A thick section stained loose in wells of solution before mounting, common for brain.Sectioning
- Free-swelling control
- Constructs cultured alongside loaded ones without loading, to separate the effect of load from time in culture.Bioreactor culture
- Freeze–thaw cycle
- Warming a frozen stock and freezing it again; each cycle kills a large part of the cells.Liquid culture & strain storage
- Frictional ratio (f/f0)
- Friction relative to a compact sphere of the same mass: about 1.2–1.3 for globular proteins, higher for elongated, flexible or glycosylated ones.Analytical ultracentrifugation
- FRiP
- Fraction of reads in peaks: how much of the library is signal rather than background.Protein–DNA binding maps
- Fraction of reads in called peaks.ATAC-seq
- FRT scar
- The 80-odd bases left behind when FLP excises a cassette between two FRT sites. Unmarked, but not seamless.Microbial genetics
- FSM / ISM
- Full splice match and incomplete splice match: categories that compare a long-read isoform with the annotated ones.Specialized RNA sequencing
- Full well / saturation
- The most electrons a pixel can hold; brighter pixels clip and lose their true intensity.Widefield fluorescence
- Fully methylated and fully unmethylated standards
- Enzymatically methylated and whole-genome-amplified DNA, usually also mixed to defined intermediate ratios, taken through the conversion alongside the samples to show that conversion and amplification both behaved.DNA methylation analysis
- Fume hood
- A ventilated enclosure that extracts chemical vapour away from the user; it does not protect sterility.Lab safety & biosafety
G
- G″ (loss modulus)
- Viscous, dissipated part of the response, in pascals.Rheology
- G′ (storage modulus)
- Elastic, recoverable part of the response, in pascals.Rheology
- G1, S, G2/M
- Phases before replication (2N), during replication, and after replication through mitosis (4N).Proliferation & cell cycle
- Gain
- The photomultiplier's amplification setting. It scales signal and detector noise together, so it sets where the signal sits in the detector's range rather than improving precision.Plate readers & fluorometry
- Gate
- A region on a plot that selects a population for further analysis.Flow cytometry & FACS
- Gate stringency
- The share of events sorted; in an unenriched population this sets the per-round enrichment, at most about the reciprocal of the gate.Phage & yeast display
- GCaMP
- A genetically encoded indicator built from circularly permuted GFP, calmodulin and the M13 peptide.Calcium imaging
- Gel fraction
- Dry mass left after the unreacted sol has been washed out, divided by the polymer mass that was cast.Hydrogel synthesis
- Gel point
- The conversion at which a spanning network first forms; for an ideal 4-arm + linear step-growth gel, 58% of matched groups.Hydrogel synthesis
- The moment during crosslinking when G′ crosses G″.Rheology
- Gene-specific primer
- Usually the reverse primer of the assay itself. Gives the lowest detection limit for one target and no cDNA for anything else.Reverse transcription
- Geometric mean of references
- Averaging several reference genes' Cq values (equivalent to a geometric mean of their copy numbers) to normalise, which also reveals whether any one of them is moving.RT-qPCR
- G-factor
- Correction for the instrument's unequal sensitivity to the two polarisations, set with a standard of known polarisation.Fluorescence polarization
- Gigaohm seal
- The tight contact between glass and membrane that makes low-noise recording possible.Patch clamp
- Glass transition
- Around −135 °C for water: below it the unfrozen fraction becomes a glass and ice cannot grow.Cryopreservation & banking
- Glow discharge
- A brief plasma treatment that makes carbon films hydrophilic so samples and stain spread evenly.TEM & SEM
- Glycerol stock
- A culture mixed with glycerol to 15–25% final and frozen at −80 °C for long-term storage.Liquid culture & strain storage
- Glyoxal
- An alternative denaturant forming a reversible adduct on guanine. Gives sharper bands, but the adduct comes off if the running buffer drifts above pH 8.Northern blot
- Gold-standard FSC
- Fourier shell correlation between two independently refined half maps; resolution is quoted where it falls to 0.143.Cryo-EM
- Gradient gel
- A resolving gel whose acrylamide percentage increases down the gel, widening the range of masses resolved in one run.SDS-PAGE
- Grafting density (σ)
- Chains attached per unit area; compared with the coil size it decides mushroom or brush.Surface modification
- Gram-variable
- A culture in which some cells stain purple and some pink, usually because older or damaged Gram-positive cells lose the dye.Gram staining
- Gravimetric check
- Weighing repeated dispenses of water on a balance and converting mass to volume with the liquid's density, to measure a pipette's accuracy and precision.Pipetting & serial dilution
- Growth promotion test
- Inoculating each medium batch with a small number of reference organisms to show it supports growth.Contamination control
- Guanidinium chloride (GdmCl)
- A strong chemical denaturant, typically used up to 6–8 M; ionic, so it also screens electrostatic interactions.Intrinsic fluorescence
- Guide RNA (sgRNA)
- The RNA that targets Cas9: about 20 bases matching the site, fused to the scaffold Cas9 binds.CRISPR-Cas9 editing
- Guide RNA synthesis
- Transcription of a short single-guide RNA from a synthetic template, the cheapest route to guide RNA for CRISPR experiments, and one where run-on and dsRNA byproducts matter for cell viability.In vitro transcription
H
- Haemolysis
- Rupture of red cells, which colours serum pink and interferes with many assays.Tissue & blood collection
- Halo
- The bright rim around objects in phase contrast; an artefact of the method that enlarges apparent outlines.Brightfield & phase contrast
- Hapten
- A molecule too small to raise an antibody response on its own; it must be conjugated to a carrier to recruit T-cell help.Antibody production
- Hardware autofocus
- Focus held by detecting the reflection of an infrared beam from the coverslip, without exposing the fluorophores.Live-cell & time-lapse
- Hardy–Weinberg check
- Comparing the observed genotype counts with those expected from the allele frequency; a strong departure usually means a technical problem such as a lost cluster, not population structure.Genotyping
- HAT selection
- Hypoxanthine–aminopterin–thymidine medium, in which only hybridomas survive because the myeloma partner lacks HGPRT.Antibody production
- Heat fixation
- Passing a completely air-dried smear briefly through a flame so the cells stick to the slide and are killed.Gram staining
- Heat inactivation
- Holding serum at 56 °C for 30 min to destroy complement activity.Media & supplements
- Heat of dilution
- The heat of injecting ligand into buffer without a binding partner, measured in a control titration and subtracted or fitted as an offset.Isothermal titration calorimetry
- Heavy and light chain
- The 50 kDa and 25 kDa bands that reduced IgG puts on a gel. They swamp any target running nearby unless the elution or the detection keeps them off the blot.Immunoprecipitation
- Hemocytometer
- Counting chamber with a ruled grid and fixed depth (Neubauer improved: 0.1 mm).Cell counting & viability
- Hertz contact
- The force–indentation relation for a sphere on an elastic half-space, F ∝ E·√R·δ^1.5.Tensile & compression testing
- HIER
- Heat-induced epitope retrieval: heating sections in buffer to reverse formalin masking.Immunohistochemistry
- High-dose hook
- Loss of signal at very high analyte concentration in one-step sandwich formats.Biosensors
- High-molecular-weight DNA
- DNA kept long enough for long-read sequencing, conventionally an N50 above about 30–50 kb. It is defined by handling, not by chemistry.Genomic DNA extraction
- Higuchi model
- Release proportional to the square root of time from a planar matrix, valid while a depletion front moves inwards.Release & degradation studies
- Hill coefficient
- The steepness of a promoter's response to its regulator; above one for a cooperative repressor, and a prerequisite for bistability.Synthetic gene circuits
- Hit rate
- Share of screened clones that are both still functional and measurably improved; the product of two opposing exponentials in mutational load.Directed evolution
- HITS-CLIP / CLIP-seq
- The high-throughput sequencing version of the original CLIP, giving peaks at the resolution of the footprint.RIP & CLIP
- Hook effect
- In one-step sandwich assays, extremely high analyte saturates both antibodies separately and paradoxically lowers the signal.ELISA
- Host-cell protein (HCP)
- Protein from the expression host that survives capture; measured by immunoassay or mass spectrometry, not by a Coomassie gel.Chromatography polishing
- Proteins from the production cells; reported in ng per mg product (ppm).Downstream processing
- HotSHOT lysis
- Digesting tissue in hot sodium hydroxide, then neutralising with Tris, to release PCR-ready DNA in under an hour.Animal genotyping
- HRP polymer
- A backbone carrying many secondary antibodies and peroxidase molecules; more sensitive than avidin–biotin and free of endogenous biotin background.Immunohistochemistry
- H-score
- Semi-quantitative score, 1×%1+ + 2×%2+ + 3×%3+, from 0 to 300.Immunohistochemistry
- HSQC
- Heteronuclear single-quantum coherence: a 2D spectrum correlating each proton with the heteroatom it is bonded to.NMR spectroscopy
- Humane endpoint
- A pre-agreed point (weight loss, clinical score) at which an animal is killed humanely to prevent further suffering.Handling & dosing
- Hybridisation isotherm
- The saturating relationship between target concentration and spot signal, set by the finite number of probe molecules on a feature.Expression microarrays
- Hydraulic resistance
- Pressure drop per unit flow of a channel; for a shallow rectangle about 12μL/(wh³).Microfluidic fabrication
- Hydrodynamic radius (Rh)
- Radius of a sphere that diffuses at the same rate as the particle, including its bound solvent; larger than the anhydrous radius and larger again for elongated or flexible molecules.Dynamic light scattering
- Hydrophobic recovery
- The return of a treated surface towards its original hydrophobicity over time.Surface modification
- Hyperbranched RCA
- Adding a primer complementary to the rolling-circle product so new strands start on it, turning a linear reaction into an exponential one with a bulk signal.Isothermal amplification
I
- IC50
- Concentration that reduces the response halfway between the fitted top and bottom (relative), or to 50% of vehicle (absolute).Viability & cytotoxicity
- IDR
- Irreproducible discovery rate: a method that ranks peaks by how consistently two replicates find them.Protein–DNA binding maps
- IgG control
- The same procedure with a non-specific antibody of the same species; the usual control in CUT&RUN and CUT&Tag.Protein–DNA binding maps
- IMAC
- Immobilised metal affinity chromatography: His-tags bind metal ions held by a chelating resin.Affinity purification
- Imidazole
- Histidine-like competitor used in IMAC wash (low) and elution (high) buffers.Affinity purification
- Imprinting
- Methylation of one parental allele only at specific loci, giving ~50% in pooled data but 0% and 100% per allele.Methylation sequencing
- In vitro transcription (IVT)
- Synthesis of RNA from a DNA template by a phage RNA polymerase in a defined buffer, outside a cell.In vitro transcription
- Inclusion body
- A dense aggregate of misfolded recombinant protein inside a bacterial cell. It pellets with the debris, so it looks like failed expression until the pellet is run on a gel.Cell lysis & protein extraction
- A dense intracellular aggregate of misfolded recombinant protein; nearly pure, usually inactive, recoverable only by solubilisation and refolding.Recombinant expression
- Indel
- Small insertion or deletion left by end joining; a size that is not a multiple of three shifts the reading frame.CRISPR-Cas9 editing
- Index (barcode)
- A short sequence identifying the sample, so many libraries can be pooled and separated afterwards (demultiplexing).Short-read sequencing
- Induction
- Switching on expression of a recombinant gene, for example with IPTG for a T7 or lac promoter.Fermentation
- Infiltration
- Replacing the clearing agent with molten wax so the whole tissue becomes solid and cuttable.Fixation & processing
- Initial rate
- The slope of the progress curve while substrate depletion is negligible (under about 10%). The only rate that obeys Michaelis–Menten kinetics.Enzyme activity assays
- Initial yield
- The amount of the first residue actually detected in cycle 1, usually 30 to 60% of the protein loaded. It sets how far the read can go.Edman degradation
- Inner-filter effect
- Loss of fluorescence because the sample itself absorbs the excitation or the emitted light, which bends a standard curve over at high concentration.Plate readers & fluorometry
- Loss of measured intensity because the sample absorbs the excitation or emitted light; keep the absorbance below about 0.1.Intrinsic fluorescence
- Inoculum effect
- A rise in MIC with the number of cells tested, strong for some β-lactams against β-lactamase producers.Antimicrobial susceptibility (MIC)
- Input
- Chromatin from the same cells, sheared the same way but not immunoprecipitated; the ChIP-seq control that carries copy number, shearing and mappability biases.Protein–DNA binding maps
- Input matching
- Putting the same mass of RNA into every reaction that will be compared, measured fluorometrically rather than by A₂₆₀.Reverse transcription
- Insert
- The sample-derived part of a library molecule, between the two adapters.Library construction
- Insertional inactivation
- Cloning an insert into a reporter gene so that the gene stops working. In blue-white screening the reporter is lacZα and the colour is lost.Bacterial transformation
- Insert:vector molar ratio
- Ratio of numbers of molecules, not masses: the mass ratio that gives it depends on the two lengths.Ligation-based cloning
- Insulation
- Defined spacers or ribozymes that make a part's behaviour independent of the sequence next to it.Synthetic gene circuits
- Insulation score
- Mean contact frequency across a window sliding along the diagonal; its minima mark domain boundaries.3D genome mapping
- Integration time
- How long the detector counts photons for one well. Because luminescence is photon counting, precision improves as the square root of the counts collected.Plate readers & fluorometry
- Integrity score
- A number from about 1 to 10 computed by an electrophoresis instrument from the whole size distribution of a sample, not just the ribosomal peaks. It is the standard way to say how intact RNA is, and it falls before the ribosomal bands look obviously wrong.RNA extraction
- Interactome
- The network of interactions in an organism, large parts of which were first mapped by two-hybrid screens at genome scale.Yeast two-hybrid
- Intercalating dsDNA dye
- A dye such as the Qubit or PicoGreen chemistry that fluoresces strongly only when stacked between base pairs, making the assay specific for intact double-stranded DNA.DNA quantification & QC
- Interconnectivity
- Whether pores open into each other, which decides whether cells and fluid can travel through the scaffold.Scaffold fabrication
- Whether pores open into each other; isolated pores cannot be reached by cells or medium.Cell seeding on scaffolds
- Interfering substance
- A buffer component the assay responds to as if it were protein, or that suppresses the response: detergents in Bradford, reducing agents and chelators in BCA, aromatic detergents at 280 nm.Protein quantification
- Internal amplification control (IAC)
- A template amplified in every tube to show that a negative is a real negative and not an inhibited reaction.Contamination control
- Internal control amplicon
- A second product in the same reaction, from primers that ignore the variant, so a missing allele-specific band can be distinguished from a failed reaction.Genotyping
- Internal standard (DIGE)
- A pooled sample labelled with a third dye and run on every gel, so every spot on every gel is measured as a ratio to the same reference.2D gel electrophoresis
- Interphase
- The white layer between the aqueous and organic phases of a phenol extraction: denatured protein with phenol trapped in it. Carrying it over puts both into your sample.Genomic DNA extraction
- Intracellular ice
- Ice forming inside a cell when cooling outpaces water loss; almost always lethal.Cryopreservation & banking
- Intron-spanning assay
- An amplicon whose primers sit in different exons, so genomic DNA cannot be amplified across it. Design-level protection against DNA contamination.RT-qPCR
- Invasion index
- Cells crossing a Matrigel-coated insert as a percentage of those crossing an uncoated one, per condition.Migration & invasion
- Ionisable lipid
- A lipid with an amine of pKa near 6.5, cationic at pH 4 and near-neutral at pH 7.4.Nanoparticle formulation
- Ionomycin
- A calcium ionophore that floods cells with calcium, used to obtain Fmax and as a positive control.Calcium imaging
- IPG strip
- Immobilised pH gradient: acrylamide with buffering groups copolymerised into the matrix, so the gradient cannot drift during a long focus.2D gel electrophoresis
- iPSC
- Induced pluripotent stem cell: a somatic cell reprogrammed to pluripotency by expressing defined transcription factors.Stem cell culture
- Irreversibly denatured plasmid
- Covalently closed DNA that spent too long in alkali and could not pair correctly again. It runs ahead of supercoiled DNA, resists restriction enzymes and is useless for transfection.Plasmid preparation
- Isoelectric point (pI)
- The pH at which a protein's net charge is zero. In a pH gradient it is the position where the protein stops moving.2D gel electrophoresis
- The pH at which a protein has no net charge: where it binds neither ion exchanger and is least soluble.Chromatography polishing
- Isoform ratio
- The relative intensity of two bands in the same lane. Needs no loading control, because both bands shared every step of the experiment.Northern blot
- Isopycnic
- A gradient run taken to equilibrium, so position reports buoyant density and is independent of how long you spin.Centrifugation
- Isopycnic separation
- Separation run to equilibrium, so each particle stops where the medium matches its own buoyant density and position no longer depends on run time.Subcellular fractionation
- Isothermal
- Held at one temperature throughout. There is no cycling, so product accumulates in time rather than in cycles.Isothermal amplification
- Isotype control
- An antibody of the same class and species as the primary but with no relevant target, used at the same concentration.Immunohistochemistry
- ITS (internal transcribed spacer)
- Spacer regions between fungal rRNA genes (ITS1, ITS2); the standard fungal barcode, highly variable in sequence and length.Amplicon & microbiome sequencing
- IVIVC
- In vitro–in vivo correlation: a validated relationship between a release profile in a tube and performance in an animal or patient.Release & degradation studies
J
- Junction PCR
- A confirmation PCR with one primer outside the homology arm and one inside the cassette, so it only amplifies if the cassette sits at the target locus.Microbial genetics
K
- ka (kon)
- Association rate constant, M⁻¹s⁻¹.SPR & BLI
- Kav
- The partition coefficient in SEC, (Ve − V0)/(Vt − V0); linear in log molecular weight over the matrix's fractionation range.Chromatography polishing
- KD
- Equilibrium dissociation constant = kd/ka, in M. Lower means tighter binding.SPR & BLI
- Calcium concentration at which half the indicator is bound; sets the range of concentrations it reports.Calcium imaging
- kd (koff)
- Dissociation rate constant, s⁻¹; complex half-life = ln2 / kd.SPR & BLI
- Ki
- The dissociation constant of the inhibitor from the enzyme (or the enzyme–substrate complex). Obtained from how the apparent Km or Vmax changes with inhibitor concentration.Enzyme activity assays
- Kill curve
- A titration of the selection drug on untransfected cells that identifies the lowest dose killing all of them in a few days.Stable cell line generation
- Kitome
- Contaminating microbial DNA from extraction kits, reagents and water, prominent in low-biomass samples.Amplicon & microbiome sequencing
- kLa
- Volumetric oxygen transfer coefficient (per hour); oxygen transfer per unit driving force.Bioreactor culture
- Knife lines
- Tears running the length of the section in the cutting direction, from a nick or debris on the edge.Sectioning
- Knockdown efficiency
- The fraction of the target removed, relative to a non-targeting control measured in the same experiment. Quote it with the method and the time point, because it is a property of both.RNA interference
- Köhler illumination
- Alignment that focuses the field diaphragm in the sample plane and centres it, giving even, glare-free light; the starting point for DIC.Brightfield & phase contrast
- Kolmogorov scale
- The size of the smallest turbulent eddies; cells are damaged when it approaches their own size.Bioreactor culture
- Korsmeyer–Peppas exponent (n)
- Power-law exponent of the release profile, used to classify the transport mechanism.Release & degradation studies
L
- Label-free quantification (LFQ)
- Comparing the same peptide's MS1 intensity, or its summed fragment intensity, between separate injections. Cheap, unlimited sample number, and the most exposed to missing values.Mass spectrometry proteomics
- Labelling density
- Gold particles per µm² of a compartment, compared between compartments and with controls.TEM & SEM
- Ladder (marker)
- A mix of DNA fragments of known sizes run alongside samples for sizing.Agarose gel electrophoresis
- Laemmli system
- The discontinuous Tris-glycine buffer system with a stacking gel at pH 6.8 over a resolving gel at pH 8.8, still the standard for protein gels.SDS-PAGE
- Lag
- Out-of-phase signal from chains that failed to advance in an earlier cycle, so the previous residue keeps appearing alongside the current one.Edman degradation
- Lag phase
- The period after seeding before cells divide again, lengthened by rough handling or very low density.Aseptic technique & passaging
- The period after inoculation before cells divide at their full rate; often quoted as where the exponential line meets the starting density.Growth curves
- Large square
- 1 × 1 mm square; at 0.1 mm depth it holds 0.1 µL.Cell counting & viability
- Leak (basal expression)
- Output of a fully repressed promoter, as a fraction of its maximum; sets how off the off state can be.Synthetic gene circuits
- Leak subtraction
- Removing the passive current using scaled small steps (a P/N protocol).Patch clamp
- Leakiness
- Expression from an inducible promoter with no inducer present; the denominator of the fold induction and the usual reason a clone is discarded.Stable cell line generation
- Leaky expression
- Product made before the inducer is added, because no promoter is fully repressed.Recombinant expression
- Library
- DNA fragments with sequencing adapters and indexes attached.Short-read sequencing
- The population of variants that actually exists in cells; capped by the transformation, not by the number of different molecules in the tube.Directed evolution
- Library complexity
- The number of distinct molecules in a library; it sets the duplicate rate at a given sequencing depth.Library construction
- The number of distinct molecules in a library; when it is low, extra reads are duplicates and add nothing.Protein–DNA binding maps
- Ligand / analyte
- Ligand is immobilised on the surface; analyte is in solution.SPR & BLI
- Ligand depletion
- Loss of free ligand to binding when protein and ligand concentrations are similar, which shrinks the observed shift.Thermal shift assays
- Removal of free ligand by binding to the labelled partner, significant when that partner is not far below KD; handled by the quadratic fit.Microscale thermophoresis
- Light scattering
- Light deflected by aggregates or particles that never reaches the detector, which an absorbance reader cannot distinguish from absorbance.Protein quantification
- Light sheet
- A thin plane of excitation light, made by a cylindrical lens or by scanning a focused beam, that lights only the focal plane of the detection objective.Light-sheet microscopy
- Limit of blank
- The positive count you get from a sample known to contain no target. Measured, not assumed, and it is what a rare-variant call must exceed.Digital PCR
- Limit of detection
- About 2 ng/µL for absorbance however carefully you read it, because the signal becomes the same size as the baseline noise; picograms per µL for a fluorescent dye.DNA quantification & QC
- The lowest allele fraction detected with a stated probability (often 95%); set by molecules counted and by background error.Exome & targeted panels
- Limit of detection (LOD)
- Lowest concentration distinguishable from a blank, conventionally 3σ of the blank divided by the calibration slope.Biosensors
- Limit of quantification
- Lowest concentration measurable with acceptable precision, conventionally 10σ over the slope.Biosensors
- Limiting dilution
- Plating cells sparsely enough that a growing well came from one cell; two rounds are the standard proof of monoclonality.Antibody production
- Limiting mobility
- Above ~20–50 kb all DNA moves at the same speed in a constant field, so sizes can't be separated without pulsed fields.Agarose gel electrophoresis
- Above roughly 20–50 kb all DNA moves at the same speed in a constant field, so very large fragments cannot be sized on a conventional gel.Southern blot
- LIMS
- Laboratory information management system: sample-centred software that registers accessions and aliquots, and tracks location, custody and consumption.Record keeping & sample tracking
- Linear dynamic range
- The range of amounts over which signal is proportional to amount, bounded by noise below and saturation or depletion above.Gel & blot imaging
- Linear extrapolation method
- Fitting denaturation data with ΔG falling linearly with denaturant concentration, and extrapolating to zero denaturant.Intrinsic fluorescence
- Linear viscoelastic region
- The range of strain where moduli do not depend on amplitude.Rheology
- Linearisation
- Cutting a plasmid downstream of the insert so the polymerase has an end to stop at. Must go to completion, and must be verified.In vitro transcription
- Linkage error
- The distance between the dye and its target set by the label (about 10–20 nm for primary plus secondary antibodies).Super-resolution
- Lipofuscin
- Autofluorescent granules that accumulate in long-lived cells; punctate, dot-sized and bright in every channel, so they mimic real spots.In situ hybridization
- Lipoplex / polyplex
- The particle formed between nucleic acid and a cationic lipid or polymer; its size and charge decide uptake.Transfection
- LLOQ / ULOQ
- Lower and upper limits of quantification: the concentration range where the curve gives accurate values.ELISA
- Local field potential (LFP)
- The low-frequency part of the extracellular signal, dominated by summed synaptic currents.Extracellular recording
- Localisation precision
- How well a single molecule's position is known, roughly the PSF width divided by √(photons), worsened by background.Super-resolution
- Lock
- The spectrometer's feedback on the deuterium signal of D₂O that keeps the magnetic field stable during long experiments.NMR spectroscopy
- Log reduction value (LRV)
- log₁₀ of impurity in over impurity out across a step.Downstream processing
- Log2 fold change
- The readout per guide: its normalised count at the end divided by its count at T0, logged.CRISPR screens
- The base-2 logarithm of the ratio of normalised expression between conditions: 1 means doubled, −1 halved.RNA-seq
- Loop
- A focal enrichment of contacts between two distant loci, often anchored by convergent CTCF sites.3D genome mapping
- Low-binding membrane
- A membrane chemistry such as PES or cellulose acetate that adsorbs only a few micrograms of protein per cm², as against 100 µg/cm² or more for nylon.Filtration & sterilization
- Lower marker
- A short fragment spiked into every well at a known concentration, used to align traces and to normalise signal between samples. Its height is one of the features the integrity algorithm uses, and a missing marker invalidates the run.RNA integrity check
- Low-pH viral inactivation
- Holding the Protein A eluate at about pH 3.5–3.7 for an hour to inactivate enveloped viruses.Downstream processing
- loxP site
- A 34 bp sequence Cre recognises: two inverted 13 bp arms around an 8 bp asymmetric spacer, which is what gives the site its direction.Other editing & transgenesis
- Luciferin kinetics
- The rise and fall of the bioluminescent signal after substrate injection; imaging is timed to its plateau or peak.In vivo imaging
- Lumry–Eyring model
- Reversible unfolding followed by an irreversible step (often aggregation), used to analyse scan-rate-dependent DSC transitions.Differential scanning calorimetry
- Lysate
- The cleared culture after infection, containing the phage, host debris and medium; clarified and stored as the working stock.Phage work
- Lysochrome
- A fat-soluble dye such as Oil Red O that stains by dissolving into lipid rather than binding.Special stains
- Lysogen
- A host carrying a temperate phage as a prophage. Lysogens give turbid plaques, and can release phage spontaneously, which shows up on a host-only control plate.Phage work
M
- m6A
- N6-methyladenosine, the most common internal mRNA modification, usually at DRACH sequence motifs.Specialized RNA sequencing
- Machine compliance
- The deformation of frame, load cell and grips, which adds to crosshead travel.Tensile & compression testing
- MAG
- Metagenome-assembled genome: a genome reconstructed from shotgun data by assembly and binning, usually needing ≥ 10× coverage.Amplicon & microbiome sequencing
- Manders' coefficients
- M1: the fraction of channel 1 signal in pixels where channel 2 is above its threshold; M2 the reverse.Image analysis
- Mapping quality (MAPQ)
- Phred-scaled confidence that a read is placed correctly; 0 means it fits equally well elsewhere.Read processing & analysis
- Marker range
- The size window between a sizing assay's lower and upper markers. Material outside it is included in the concentration but cannot be sized.DNA quantification & QC
- Mass calibration
- Converting flight time to mass using a standard of known masses spotted on the same target; it drifts and is redone regularly.Biochemical identification
- Mass ladder
- A DNA ladder with stated amounts per band, used as an intensity standard.Gel & blot imaging
- Mass swelling ratio (Qm)
- Swollen mass at equilibrium divided by dry polymer mass.Hydrogel synthesis
- Master cell bank (MCB)
- A small set of vials frozen once from an authenticated, tested culture at low passage.Cryopreservation & banking
- Master (mould)
- The wafer carrying raised resist features from which PDMS replicas are cast.Microfluidic fabrication
- Matched matrix diluent
- A standard diluent formulated to behave like the sample matrix, so the standard curve carries the same interference as the samples.Multiplex immunoassays
- Matrigel
- A basement-membrane extract from a mouse sarcoma, rich in laminin and collagen IV, that gels at 37 °C and supports organoid growth.3D culture & organoids
- A basement-membrane extract from a mouse sarcoma, rich in laminin and collagen IV, used as the invasion barrier.Migration & invasion
- Matrix effect
- A change in the assay's response caused by the sample's buffer rather than its protein. The reason standards and blanks are made in the sample buffer.Protein quantification
- Interference from other components of the sample (serum proteins, lipids) that changes the signal.ELISA
- Matrix (MALDI)
- A small aromatic acid that co-crystallises with the sample, absorbs the laser energy and transfers protons to the proteins.Biochemical identification
- Maturation
- Folding and chromophore formation after translation; until it is complete the protein is not fluorescent.Fluorescent proteins & dyes
- Maximum tolerated dose (MTD)
- The highest dose that does not cause unacceptable toxicity, set in a small pilot study.Handling & dosing
- M-bias
- Methylation level plotted by position in the read; deviations at read ends reveal end-repair or adapter artefacts to clip.Methylation sequencing
- Mc
- Average molecular weight of the chain segments between crosslinks.Hydrogel synthesis
- McFarland standard
- A turbidity reference used to standardise bacterial suspensions; 0.5 McFarland is roughly 1–2 × 10⁸ CFU/mL.Biochemical identification
- A turbidity reference for bacterial suspensions; 0.5 McFarland is about 1–2 × 10⁸ CFU/mL for E. coli.Antimicrobial susceptibility (MIC)
- Mean depth (coverage)
- Average number of distinct reads covering each base, after duplicates and unmapped reads are removed.Whole-genome sequencing
- Mean residue weight (MRW)
- Protein mass divided by the number of peptide bonds (residues − 1), typically 110–115 Da.Circular dichroism
- Mechanotransduction
- Conversion of mechanical cues such as shear or stretch into cell signalling and gene expression.Organ-on-chip
- Melt curve
- Fluorescence against temperature after cycling, used with a dsDNA dye to check that one product was made. Its derivative peaks at the product's Tm.Quantitative PCR (qPCR)
- Melting temperature (Tm)
- The stability of the oligo/RNA duplex. Sugar modifications raise it, which is how a shorter, more potent oligo is made, and how off-target duplexes become stable too.Antisense oligonucleotides
- Membrane potential dye
- A lipophilic cation, such as MitoTracker or TMRM, that concentrates in mitochondria in proportion to their potential.Fluorescent proteins & dyes
- Mendelian ratio
- The 1 : 2 : 1 wild type : heterozygote : knockout proportion expected from a heterozygous cross.Animal genotyping
- Meniscus
- Air–solution boundary at the top of the column, the origin from which sedimentation is measured; fitted in the analysis.Analytical ultracentrifugation
- Merodiploid resolution
- The second crossover that excises an integrated plasmid, leaving either the new allele or the original one behind.Microbial genetics
- Mesh size (ξ)
- The typical spacing between chains in the swollen network, usually a few to tens of nanometres.Hydrogel synthesis
- Metagene distribution
- Where peaks fall across a normalised transcript: 5′ UTR, CDS, 3′ UTR, intron. A sanity check against what the protein is known to do.RIP & CLIP
- Method suitability
- Showing that the sample does not inhibit growth of spiked organisms (for example through carried-over antibiotic).Contamination control
- Methylation-specific PCR (MSP)
- Two PCRs per sample on converted DNA, with primers that match either the methylated or the unmethylated converted sequence at several CpGs. Reports presence or absence, not quantity.DNA methylation analysis
- Methylene blue staining
- Reversible staining of the membrane after transfer, used to record the ribosomal bands and the ladder positions and to confirm that transfer worked.Northern blot
- MFI
- Median fluorescence intensity: the raw readout of a bead-based assay, the median over the beads of one region in that well.Multiplex immunoassays
- Median fluorescence intensity of a population; a measure of how much antigen cells carry.Flow cytometry & FACS
- mg/kg
- Dose per kilogram of body weight; the volume follows from the animal's weight and the solution's concentration.Handling & dosing
- MIC
- Minimum inhibitory concentration: the lowest drug concentration that prevents visible growth of a standard inoculum under standard conditions.Antimicrobial susceptibility (MIC)
- Michaelis–Menten fit
- Non-linear least-squares fit of rates against substrate to v = Vmax[S]/(Km + [S]). Preferred over linearised plots.Enzyme activity assays
- Microsampling
- Collecting 10–30 µL per time point, so serial samples stay within volume limits.Tissue & blood collection
- Miles–Misra (drop) method
- Counting from small drops of each dilution spotted onto one plate, rather than one plate per dilution.CFU counting
- Miller units
- β-galactosidase activity normalised to cell density and reaction time, so numbers from different cultures can be compared.Yeast two-hybrid
- Minimal promoter
- A TATA box and start site with no enhancers; on its own it gives low basal transcription.Reporter assays
- Minimum detectable effect
- The noise floor times the hit threshold. Testing 19,000 genes pushes the threshold out to roughly 4.5 standard deviations.CRISPR screens
- Minus-RT control
- The same qPCR reaction with the reverse transcriptase left out. Any signal comes from DNA, so the gap in cycles between the minus-RT and the full reaction is the only direct measure of whether residual genomic DNA matters for that assay.RNA extraction
- The reaction without the enzyme. Anything amplifying from it was DNA, so it is the control that validates a cDNA measurement.Reverse transcription
- MIQE
- The published minimum information set for reporting a qPCR experiment: efficiency, controls, reference genes, replicate structure and analysis settings.Quantitative PCR (qPCR)
- The reporting guidelines for quantitative PCR experiments: which controls, efficiencies, normalisers and replicate structures have to be stated in a paper.RT-qPCR
- Mispriming
- Primers binding partly matching sites, which gives off-target bands.PCR
- Missed cleavage
- A lysine or arginine that trypsin failed to cut, leaving a longer peptide. Splits one peptide's signal across several forms.Mass spectrometry proteomics
- Missing wedge
- The region of Fourier space a tomogram never samples because the stage cannot tilt to ±90°; it elongates features along the beam.Cryo-EM
- Mitochondrial fraction
- Share of reads from mitochondrial DNA, which is discarded; high values waste sequencing.ATAC-seq
- Mitomycin C
- A DNA cross-linker used briefly before a scratch to block cell division so closure reflects migration.Migration & invasion
- Mixed base
- A position with two overlapping peaks; written as an IUPAC code (R = A/G, Y = C/T) by callers that report them.Sanger sequencing
- Mixing time
- The delay in a NOESY during which NOEs build up; too long and magnetisation relays through intermediate protons (spin diffusion).NMR spectroscopy
- mL/kg
- Volume per kilogram of body weight, the unit route limits are written in; numerically the same as µL/g.Handling & dosing
- Mn and mass loss
- Number-average molar mass, which falls immediately, and dry mass, which falls only once fragments are soluble.Release & degradation studies
- Mobile fraction
- The share of molecules that exchange into a bleached region over the experiment; the rest are immobile on that timescale.FRET, FRAP & FLIM
- Mobility
- How fast a fragment moves per unit field; falls with log(size) and with gel percentage.Agarose gel electrophoresis
- Modulation contrast
- How strongly the SIM stripe pattern is imprinted on the raw images; low modulation gives noisy, artefact-prone reconstructions.Super-resolution
- MOI
- Multiplicity of infection for a viral shRNA: functional particles per cell. Transduction is Poisson, so MOI sets both the fraction transduced and the copies per cell.RNA interference
- Multiplicity of infection: infectious units added per cell present at the time of transduction.Viral transduction
- Molar ratio
- Total ligand over total protein in the cell after each injection, the x-axis of the isotherm.Isothermal titration calorimetry
- Molarity
- Moles of solute per litre of solution (M = mol/L).Buffer & media preparation
- Molecules per volume (nM); what loading concentration and pooling are set in.Library QC & pooling
- Molarity from mass
- nM = ng/µL × 10⁶ ÷ (660 × bp). The 660 g/mol per base pair is an average; the bp has to come from a size measurement.DNA quantification & QC
- Molten globule
- A compact state with much native secondary structure but loose side-chain packing: far-UV close to native, near-UV signal largely lost.Circular dichroism
- Monoclonality
- Evidence, not an assumption, that a line descends from one cell: a day-1 image, index sorting records, or two rounds of cloning.Stable cell line generation
- Monod equation
- μ = μmax·S/(Ks + S): growth rate saturating with substrate concentration.Fermentation
- Monodispersity (CV)
- Standard deviation of droplet diameter over its mean; a good junction gives a few per cent or less.Droplet microfluidics
- Monomeric FP
- A fluorescent protein engineered not to dimerise (e.g. mEGFP with A206K, mCherry), so it does not cross-link the protein it tags.Fluorescent proteins & dyes
- Mordant
- A metal ion (aluminium for Harris haematoxylin, iron for Weigert's) that links the dye to the tissue.H&E staining
- Mosaicity
- Angular spread of the crystal's ordered blocks. High mosaicity smears spots over a wider rotation.X-ray crystallography
- Motion correction and dose weighting
- Aligning the frames of each movie to undo beam-induced motion, and down-weighting high frequencies in later, more damaged frames.Cryo-EM
- MST power
- Infrared laser power, which sets how far the spot heats; higher power gives a larger signal but more heating.Microscale thermophoresis
- Mullins effect
- Softening of an elastomer or tissue after the first loading cycles; the reason tissues are preconditioned.Tensile & compression testing
- Multi-electrode array (MEA)
- A dish or chip with tens to thousands of embedded electrodes that record from a culture or slice grown on it.Extracellular recording
- Multiplet (doublet)
- A barcode that holds two or more cells; heterotypic doublets mimic intermediate states, homotypic ones are invisible.Single-cell RNA-seq
- Multiplexing
- Reading several targets in one well using probes with different fluorophores. Needs matched efficiencies and a check that the assays do not compete.Quantitative PCR (qPCR)
- Multiplicity of infection (MOI)
- Virions per cell. At MOI 0.3 about a quarter of cells are infected and ~86% of those carry a single guide.CRISPR screens
- Mushroom and brush
- Sparse grafted chains are separate coils (mushrooms); dense ones overlap and stretch away from the surface (brush).Surface modification
- Mutagenic primer
- An oligonucleotide carrying the intended change in its middle, with enough correct sequence on each side to anneal: about 10–15 nt per side for a substitution, 15–20 for an insertion or deletion.Site-directed mutagenesis
- Mutant competitor
- Unlabelled DNA with the site mutated; it should leave the shifted band intact.EMSA (gel shift)
- Mutational load
- Substitutions per gene, usually quoted per kilobase of coding sequence or as amino-acid changes per protein.Directed evolution
- MWCO
- Molecular weight cut-off: the mass at which a membrane retains a stated fraction (often 90%) of a test solute. A nominal label on a pore-size distribution.Dialysis & buffer exchange
- Mycoplasma
- Wall-less bacteria (Mollicutes) that contaminate cell cultures without visible signs; unaffected by penicillin.Contamination control
N
- N1-methylpseudouridine (m1Ψ)
- A uridine analogue that replaces U entirely in therapeutic mRNA, lowering innate sensing and increasing translation.In vitro transcription
- N50
- The fragment length above which half the mass of the DNA lies. A more useful description of a size distribution than a mean, because mass is dominated by the long molecules.Genomic DNA extraction
- The fragment length above which half the mass of the sample lies. More useful than a mean for a skewed distribution, and the number long-read protocols specify.DNA quantification & QC
- nanoDSF
- Label-free thermal shift assay following intrinsic tryptophan fluorescence at 330 and 350 nm in capillaries.Thermal shift assays
- NASBA / HDA / SDA
- Other isothermal chemistries built on the same idea with different enzymes (a helicase, a nicking enzyme, or an RNA-based cycle) used where their particular format suits.Isothermal amplification
- Near miss
- An incident that could have caused harm but did not; reporting it is how causes get fixed.Lab safety & biosafety
- Near-UV CD
- The 250–320 nm region, from aromatic side chains and disulfides in a fixed environment; reports tertiary structure.Circular dichroism
- Necrotic core
- The dead centre of a large spheroid, where oxygen and nutrients do not reach.3D culture & organoids
- Negative stain
- A heavy-metal salt that dries around particles so they show as light shapes on a dark background.TEM & SEM
- Negative-control probe
- A probe matching no sequence in the sample, or a codeword matching no probe; its count is the false-decode rate of the run.Spatial transcriptomics
- Network burst
- A brief period when many electrodes across a culture fire together; a hallmark of a mature, connected network.Extracellular recording
- Neuropil
- The tangle of processes around cell bodies; its fluorescence contaminates somatic ROIs in tissue.Calcium imaging
- Neutral buffered formalin (NBF)
- 10% formalin (about 4% formaldehyde) in phosphate buffer at pH 7; the standard histology fixative.Fixation & processing
- Neutral loss
- Loss of the modification as an uncharged molecule during collisional fragmentation, for example 98 Da of phosphoric acid from a phosphopeptide, which consumes signal that would have gone into backbone ions.Post-translational modification analysis
- Nitrocellulose wicking time
- Seconds for the front to travel 4 cm; a higher number is a slower membrane and usually a more sensitive strip.Biosensors
- No-call
- The honest outcome when the data do not place a sample in a genotype. A no-call is a result; a miscall is not.Genotyping
- NOE
- Nuclear Overhauser effect: transfer of magnetisation between protons through space, proportional to r⁻⁶.NMR spectroscopy
- Non-CpG cytosine
- A cytosine outside a CpG dinucleotide. Essentially unmethylated in vertebrate somatic tissue, so it serves as the built-in conversion control inside a read.DNA methylation analysis
- Non-descanned detector
- A detector placed close to the objective that collects emitted light without sending it back through the scanner and pinhole, so scattered photons still count.Confocal microscopy
- Non-ionic detergent
- A detergent with an uncharged head group, such as NP-40, Triton X-100 or digitonin. It dissolves lipid without competing with the charge and hydrophobic interactions that hold complexes together.Cell lysis & protein extraction
- Non-specific binding
- Signal from anything that sticks other than the analyte binding its receptor.Biosensors
- Non-specific competitor
- Unrelated DNA such as poly(dI·dC) added in excess to absorb weak, sequence-independent binding.EMSA (gel shift)
- Non-targeting guide
- A guide matching nothing in the genome. A thousand of them define the distribution a guide follows when the gene does nothing.CRISPR screens
- Normalisation
- Putting arrays or channels on a common scale before anything is compared. Part of the measurement, and different methods remove different artefacts.Expression microarrays
- Calibrating the detectors at different angles against the 90° detector with an isotropic scatterer, so that they agree for small molecules.SEC-MALS
- Normalisation reporter
- A co-transfected, constitutively expressed second reporter used to correct for transfection efficiency and cell number.Reporter assays
- No-template control (NTC)
- A qPCR well with no library, showing that primers and reagents are free of contaminating library.Library QC & pooling
- N/P ratio
- Moles of polymer amine nitrogen per mole of DNA phosphate: the quantity that is actually optimised when a PEI transfection is titrated.Transfection
- Moles of ionisable amine per mole of nucleic-acid phosphate; the main control on nucleic-acid encapsulation.Nanoparticle formulation
- NRMSD
- Normalised root-mean-square deviation between a spectrum and its fit; values above about 0.1 suggest the fit cannot be trusted.Circular dichroism
- NTC (no-template control)
- A tube with every reagent except template. It must stay blank; a band means contamination.PCR
- Nuclear-seeded cell mask
- Cell outlines grown from the DAPI-stained nuclei, used to assign each spot to a cell without reference to the spots themselves.Proximity ligation assay
- Nucleofection
- Electroporation with cell-type-specific solutions and pulse programmes designed to deliver cargo to the nucleus with high survival.Transfection
- Nucleosome-free region (NFR)
- Open DNA between nucleosomes, typically at promoters and enhancers; gives fragments shorter than about 100 bp.ATAC-seq
- Nucleotide-loading control
- In a pull-down for an active GTPase, the same prey loaded with GDP. A band that disappears when the nucleotide is swapped is recognition; a band that does not is surface binding.Pull-down assays
- Nullcline
- The set of states where one variable is at steady state; crossings of two nullclines are the circuit's steady states.Synthetic gene circuits
- Numerical aperture (NA)
- n × sin of the objective's half-angle; it sets resolution (∝ λ/NA) and light collection.Widefield fluorescence
- Nyquist sampling
- Pixels at least 2–3 times smaller than the resolution, so the image preserves what the optics deliver.Widefield fluorescence
O
- Obligate heterodimer
- FokI mutated so that each monomer can only pair with its partner, not with a copy of itself. The standard way to cut off-target cleavage.Other editing & transgenesis
- OCT compound
- A water-soluble glycol and resin embedding medium that supports tissue for frozen sectioning.Fixation & processing
- OD600
- Light scattered out of a 600 nm beam by a cell suspension; a proxy for biomass, linear only at low density.Growth curves
- Off-rate selection
- Loading the library, then washing in the presence of excess soluble target so that only slowly-dissociating clones remain bound.Phage & yeast display
- Off-target
- A site resembling the guide that also gets cut; fewer when the nuclease is short-lived and the guide is unique.CRISPR-Cas9 editing
- Off-target cleavage
- RNase H cutting transcripts the gapmer matches imperfectly. Scales with affinity and with intracellular concentration, and is the mechanism behind high-affinity gapmer hepatotoxicity.Antisense oligonucleotides
- Off-target effect
- Repression of transcripts other than the intended one, mostly through seed complementarity in their 3′ UTRs. Scales with guide concentration.RNA interference
- Oil immersion
- Using a 100× objective with immersion oil between lens and slide, giving the resolution needed to see the shape and arrangement of bacteria.Gram staining
- Oligo walk
- Screening many oligos tiled along a transcript, because activity varies enormously with site and cannot be predicted reliably.Antisense oligonucleotides
- Oligo(dT)
- A primer of 18–25 thymidines that anneals to the poly-A tail. Selects polyadenylated RNA and starts every cDNA at the 3′ end.Reverse transcription
- On-target rate
- Fraction of reads or bases falling in the targeted regions (sometimes counted with a small flank).Exome & targeted panels
- Open circle
- A plasmid with a nick in one strand, so the supercoiling has relaxed. It still digests and sequences, but it migrates more slowly and transfects less well.Plasmid preparation
- Optical density (OD)
- The same number as absorbance, but used when the loss of light is mostly scattering rather than absorption, as in OD600 of a culture.UV-Vis spectrophotometry
- Optical path difference
- The extra distance light effectively travels through a denser object, refractive-index difference × thickness; what phase contrast and DIC make visible.Brightfield & phase contrast
- Optical section
- The thickness (axial FWHM) of the slab that contributes to a confocal image; set by NA, wavelength and pinhole size.Confocal microscopy
- Optical window
- Roughly 650–900 nm, where haemoglobin and water absorb least and tissue is most transparent.In vivo imaging
- Organoid
- A self-organising 3D structure grown from stem cells that reproduces some of the architecture and cell types of an organ.3D culture & organoids
- Orientation
- Which end of the bait is tethered. A tag at the wrong terminus, or on too short a linker, can occlude the very surface the experiment is testing.Pull-down assays
- Orientation index
- Mean cos 2θ of the cells' long axes to the flow: 0 for random orientation, 1 for perfect alignment.Organ-on-chip
- oriT
- The origin of transfer on a conjugative or mobilisable plasmid: the sequence a donor's transfer machinery nicks and pumps into a recipient.Microbial genetics
- Orthogonal validation
- Independent evidence that the antibody binds the intended target, ideally by removing the antigen genetically.Antibody production
- Orthogonality
- Freedom from cross-talk between parts, and between the circuit and the host's own regulation.Synthetic gene circuits
- Oscillating perfusion seeding
- Pumping the cell suspension back and forth through a scaffold sealed in a chamber, so all the liquid passes through the pores.Cell seeding on scaffolds
- Osmotic support
- Sucrose or mannitol in the homogenisation medium at a concentration that keeps organelles from swelling and bursting while the cell is being broken.Subcellular fractionation
- OTR and OUR
- Oxygen transfer rate into the liquid and oxygen uptake rate by the cells, both in mmol/L/h.Bioreactor culture
- Otsu threshold
- An automatic threshold that best separates an image's histogram into two classes.Image analysis
- Outer membrane
- The second, lipopolysaccharide-containing membrane of Gram-negative bacteria, which the decolorizer dissolves.Gram staining
- Outgrowth (phenotypic expression)
- The 20–60 min in rich medium at 37 °C between getting the DNA in and meeting the antibiotic, during which the resistance protein is made.Bacterial transformation
- Output titre
- Infectious phage recovered from a round; meaningful only beside the titre from the no-target well.Phage & yeast display
- Over-drying
- Drying a nucleic acid pellet past the point where the alcohol has gone, which makes it hard or impossible to redissolve.Precipitation
- Overflow metabolism
- Excretion of acetate (E. coli) or ethanol (yeast) when glucose uptake exceeds respiratory capacity.Fermentation
- Overlap extension
- Making the change in two overlapping halves and then joining them through their shared sequence, instead of amplifying the whole plasmid in one reaction.Site-directed mutagenesis
- Overlap (homology arm)
- The 15–40 bp of shared sequence at the ends of two neighbouring pieces, which defines their junction in overlap assembly.Seamless assembly
- Overnight culture
- A small liquid culture, typically 2–5 mL, grown 12–16 h from a single colony to early stationary phase.Liquid culture & strain storage
- Overproduction inhibition
- Transposition falling as transposase rises past an optimum. Strong for Sleeping Beauty, so the enzyme-to-donor ratio has to be titrated.Other editing & transgenesis
- Oxonium ion
- A low-mass sugar fragment (for example 204.087 for HexNAc) produced when a glycan fragments. Diagnostic that a spectrum came from a glycopeptide, and useless for locating the site.Post-translational modification analysis
- Oxygen inhibition
- Dissolved oxygen scavenging radicals, delaying cure and leaving a tacky surface.Hydrogel synthesis
P
- padj
- A Benjamini–Hochberg adjusted p-value; calling genes at padj < 0.05 controls the false-discovery rate at 5%.Read processing & analysis
- pAG-MNase / pAG-Tn5
- Protein A/G fused to micrococcal nuclease or to Tn5 transposase: the enzymes that CUT&RUN and CUT&Tag tether to the antibody.Protein–DNA binding maps
- PAM
- Protospacer-adjacent motif, NGG for SpCas9. Without it, Cas9 will not cut, however good the guide.CRISPR-Cas9 editing
- Panel of normals
- Calls from many unrelated normal samples, used to remove recurrent technical artefacts from somatic call sets.Whole-genome sequencing
- Panel validation
- Demonstrating specificity, recovery, linearity and precision for every analyte in the combination actually being run, as opposed to in each assay separately.Multiplex immunoassays
- Panniculus carnosus
- The thin muscle layer under rodent skin that drives rapid wound contraction; humans largely lack it.Disease & implant models
- Paracrine signalling
- Signalling by secreted factors between nearby cells, the interaction an indirect co-culture isolates.Co-culture
- PAR-CLIP
- Photoactivatable-ribonucleoside-enhanced CLIP: metabolic labelling with 4-thiouridine and 365 nm crosslinking, read out as T→C conversions.RIP & CLIP
- Parent–child identifiers
- A scheme in which each aliquot gets its own unique identifier linked to the sample it came from, so freeze–thaw history and consumption are per tube.Record keeping & sample tracking
- Partial digest
- A digest in which only some copies of a site were cut, so signal appears at the size defined by the next site out as well as at the expected size.Southern blot
- Partial specific volume (v̄)
- Volume increment per gram of solute, ≈ 0.73 mL/g for proteins and lower for carbohydrate; it sets the buoyancy factor 1 − v̄ρ.Analytical ultracentrifugation
- Partial-volume effect
- Blurring of a structure over neighbouring voxels when it is not much larger than the voxel.In vivo imaging
- Partition
- One of the thousands of independent sub-reactions, a droplet or a chamber. Its volume is the unit that converts a count into a concentration.Digital PCR
- Pass / subread
- One traversal of the insert by the polymerase; several are combined into the consensus read.Long-read sequencing
- Passage number
- How many times a culture has been subcultured since it was established or thawed; written on every flask.Aseptic technique & passaging
- Passenger (hitchhiker)
- A neutral or mildly deleterious substitution that travels with a beneficial one because they are linked on the same clone.Directed evolution
- Path length
- The distance the beam travels through the sample: 10 mm in a standard cuvette, about 1 mm on a microvolume pedestal, and whatever the liquid depth happens to be in a plate well.UV-Vis spectrophotometry
- The distance light travels through the sample. 1 cm in a standard cuvette; in a plate it is the depth of liquid, about 0.6 cm for 200 µL in a 96-well plate.Protein quantification
- The depth of liquid the light passes through. 200 µL in a 96-well plate is about 0.62 cm, so a plate absorbance is not a cuvette absorbance.Enzyme activity assays
- Path length in a well
- The depth of liquid: about 0.62 cm for 200 µL in a flat-bottom 96-well. It sets the absorbance and must be known to convert a plate reading into a concentration.Plate readers & fluorometry
- PBMC
- Peripheral blood mononuclear cells: lymphocytes and monocytes, the cells with a single round nucleus that collect at a Ficoll interface.Primary cell isolation
- PBS and RTT
- The primer-binding site the nicked strand anneals to, and the template copied into the nick. Their lengths are the main design variables in prime editing.Base & prime editing
- PCR inhibitor
- Anything in the sample that blocks the polymerase: salt, heme, collagen, residual alkali or active proteinase K.Animal genotyping
- PDMS
- Poly(dimethylsiloxane), the silicone elastomer used for most research chips; usually mixed 10 : 1 base to curing agent.Microfluidic fabrication
- PE2 / PE3 / PE3b
- Nicking strategies: no second nick, a nick on the other strand, or a nick that only occurs once the edit is installed. PE3 raises efficiency and indels; PE3b raises efficiency with fewer indels.Base & prime editing
- Peak
- A region with significantly more reads than the control predicts, reported with a fold enrichment, p-value and q-value.Protein–DNA binding maps
- Peak calling
- Finding regions where immunoprecipitated reads are enriched over a background model. The choice of background (input, mock, or nothing) largely determines the answer.RIP & CLIP
- Pearson's correlation coefficient
- Covariance of two channels' intensities divided by the product of their standard deviations, from −1 to 1.Image analysis
- pegRNA
- A prime-editing guide extended with a primer-binding site and a reverse-transcriptase template carrying the edit.Base & prime editing
- Penetration coefficient (K)
- The constant in d = K·√t describing how far a fixative diffuses in a given time; about 0.8 mm/√h for formaldehyde.Fixation & processing
- Peptidoglycan
- The mesh of sugar chains cross-linked by short peptides that forms the bacterial cell wall; many layers thick in Gram-positive cells, one or two in Gram-negative ones.Gram staining
- Perfusion
- Flushing an organ's blood vessels with buffer before removal, to clear blood cells from the tissue.Primary cell isolation
- Permeabilisation
- Making membranes porous with detergent or alcohol so antibodies can enter.Immunofluorescence
- Permeabilisation time
- How long the section is digested before capture. Too short loses transcripts, too long lets them diffuse sideways and blurs the map.Spatial transcriptomics
- Phagemid and helper phage
- A plasmid carrying the fusion plus a phage supplying wild-type coat proteins, which is how monovalent display is achieved.Phage & yeast display
- Phase problem
- The detector records intensities, the squares of the wave amplitudes, but not their phases; a map needs both.X-ray crystallography
- Phase ring / annulus (Ph1, Ph2, Ph3)
- The matched pair of rings in the objective and the condenser; the condenser setting must match the number engraved on the objective.Brightfield & phase contrast
- Phasor plot
- A fit-free representation of decays as points (g, s); single exponentials lie on a semicircle and mixtures inside it.FRET, FRAP & FLIM
- Phenol red
- pH indicator in most media: yellow below ~6.8, red near 7.4, purple above ~7.8.Media & supplements
- Phenyl isothiocyanate (PITC)
- The Edman reagent. Couples to a free N-terminal amine under basic conditions so that acid can then cleave off just that one residue.Edman degradation
- phi29 polymerase
- A highly processive, mesophilic polymerase from a bacteriophage, used for rolling-circle amplification at about 30 °C and inactivated above 37 °C.Isothermal amplification
- PhiX
- A well-characterised viral library spiked in as a control and to add base diversity.Short-read sequencing
- Phosphatase inhibitor
- Vanadate for tyrosine phosphatases, fluoride, β-glycerophosphate or okadaic acid for serine/threonine phosphatases. Protease cocktails do not substitute for them.Cell lysis & protein extraction
- Phosphatidylserine (PS)
- A phospholipid normally kept on the inner leaflet; exposed on the outer leaflet early in apoptosis as an 'eat me' signal.Apoptosis assays
- Photobleaching
- Irreversible loss of fluorescence with light dose; it makes later frames dimmer than earlier ones.Widefield fluorescence
- Irreversible destruction of the fluorophore by light; each protein and dye has a characteristic photostability.Fluorescent proteins & dyes
- Phototoxicity
- Damage to living cells caused by illumination, largely through reactive oxygen species; it grows with the total light dose.Live-cell & time-lapse
- Phred quality (Q)
- Log-scaled probability that a base call is wrong: Q20 = 1%, Q30 = 0.1%.Short-read sequencing
- −10·log10 of the probability a base call is wrong: Q30 means 1 error in 1,000.Read processing & analysis
- Physical : infectious ratio
- Particles (or genomes) per transducing unit; often 100–1000 for lentivector and 10³–10⁴ genomes per transduction for AAV.Viral transduction
- Picoinjection
- Adding a controlled small volume of reagent into droplets as they pass an electrified nozzle.Droplet microfluidics
- Pivot scanning
- Rocking the sheet through a small angle during each exposure so that shadows cast from different angles average out.Light-sheet microscopy
- pKa
- The pH at which a weak acid is half dissociated; the centre of its buffering range.Buffer & media preparation
- Plaque purification
- Picking a single plaque into buffer and re-plating it, repeated two or three times, to get a clonal phage stock.Phage work
- Plateau
- The late phase where product stops doubling because reagents run low and the enzyme loses activity.PCR
- Plex
- The number of analytes measured simultaneously. Cross-reactivity risk grows with its square, because every detection antibody meets every capture reagent.Multiplex immunoassays
- Pluripotency
- The ability to give rise to cells of all three germ layers; maintained by OCT4, SOX2 and NANOG and shown by markers such as TRA-1-60 and SSEA-4.Stem cell culture
- Pluronic F-68
- A non-ionic surfactant that protects cells from bubble rupture at the gas–liquid interface.Bioreactor culture
- Point spread function (PSF)
- The image of a point source; deconvolution needs one matching the real optics, measured with beads or computed carefully.Image analysis
- Point streaking
- A vertical tail above a spot, caused by free cysteine thiols re-oxidising during the second dimension. Alkylation after reduction prevents it.2D gel electrophoresis
- Poisson correction
- λ = −ln(1 − p): the step that accounts for partitions holding more than one molecule. Without it, high concentrations are systematically undercounted.Digital PCR
- Poisson counting error
- The scatter of a count of independent events: a relative standard error of about 1/√N, where N is the total number of colonies counted.CFU counting
- Poisson loading
- Random occupancy of droplets by discrete particles, with mean λ = concentration × droplet volume.Droplet microfluidics
- Polarisation (mP)
- (I∥ − G·I⊥)/(I∥ + G·I⊥) × 1000: the excess of emission parallel to the excitation over perpendicular.Fluorescence polarization
- Polishing
- Further purification steps (SEC, ion exchange) after the affinity capture.Affinity purification
- Purification steps after capture, aimed at aggregate, product-related variants, host-cell protein, DNA and endotoxin rather than at bulk purification.Chromatography polishing
- Poly(A) tailing
- Adding the 3′ tail, either encoded in the template or added enzymatically after transcription with E. coli poly(A) polymerase.In vitro transcription
- Polyacid (PMA/PTA)
- Phosphomolybdic or phosphotungstic acid; displaces small red dyes from collagen so a larger blue dye can bind.Special stains
- Polyclonal pool
- The mixed population of independent integrants left after selection, before any cloning.Stable cell line generation
- Polydispersity index (PDI)
- Width of the size distribution from DLS cumulant analysis, roughly the square of the relative standard deviation of diameter.Nanoparticle formulation
- Polymerase read length
- The total sequence a polymerase produces before it stops; it bounds the number of passes.Long-read sequencing
- Ponceau S
- A reversible red total-protein stain for membranes. Photographed before blocking, it separates a transfer failure from an antibody failure.Western blot
- Population doubling level
- Cumulative number of doublings since a culture began; a more exact measure of age than passage number.Aseptic technique & passaging
- Population spike
- The summed action potentials of many neurons firing together after a large synaptic response.Extracellular recording
- Pore occupancy
- The share of active nanopores reading a strand at a given moment rather than waiting for one.Long-read sequencing
- Pore shear stress
- The drag of flowing medium on cells lining the pores; a few mPa is tolerated, tens of mPa start to detach newly attached cells.Cell seeding on scaffolds
- Pore volume
- The volume of liquid a scaffold can hold, porosity times its bulk volume.Cell seeding on scaffolds
- Poroelasticity
- Rate dependence of a water-filled network caused by fluid flowing through it as it deforms.Tensile & compression testing
- Porogen
- A sacrificial particle, such as salt or sugar, that templates pores and is removed afterwards.Scaffold fabrication
- Porosity
- The fraction of a scaffold's volume that is empty space.Scaffold fabrication
- The void fraction of the scaffold's volume; it sets how much liquid the scaffold holds.Cell seeding on scaffolds
- Porous membrane
- A thin PDMS, PET or polycarbonate sheet with micropores separating the two compartments of a barrier chip.Organ-on-chip
- Position effect
- Expression of an integrated cassette depending on where it landed, which is why clones from one transfection differ and drift apart over weeks.Other editing & transgenesis
- The influence of the integration site on how strongly and how stably the cassette is expressed.Stable cell line generation
- Positive selection
- Killing nearly everything, so survivors are enormously enriched. Huge fold changes, but a brutal sampling bottleneck.CRISPR screens
- Post-exposure bake
- The bake that completes acid-catalysed crosslinking in exposed SU-8 before development.Microfluidic fabrication
- Post-nuclear supernatant
- What is left after a low-speed spin that removes nuclei and unbroken cells but keeps membranes and organelles in suspension.Cell lysis & protein extraction
- What is left after the first low-speed spin: everything except nuclei and unbroken cells. The starting material for the mitochondrial spin.Subcellular fractionation
- Post-thaw recovery
- Viable, attached (or growing) cells some hours after thawing, as a fraction of those frozen; more honest than immediate dye exclusion.Cryopreservation & banking
- Pour plate
- Up to 1 mL of a dilution mixed with about 20 mL of molten agar cooled to 45–50 °C in an empty dish, swirled and allowed to set.Plating & streaking
- Power
- The chance of detecting an effect of a given size if it is real. Conventionally 80%, which still means one run in five misses a true effect.Experimental design & controls
- Precursor and fragment (MS1 / MS2)
- The intact peptide ion selected for fragmentation, and the backbone fragments recorded from it. MS1 gives mass and abundance; MS2 gives sequence.Mass spectrometry proteomics
- Prefilter
- A coarse layer above the sterilising membrane that retains aggregates and lipid, raising throughput without changing the retention rating.Filtration & sterilization
- Pre-running
- Running the native gel before loading to remove persulfate and establish an even ion distribution.EMSA (gel shift)
- Pre-specification
- Writing down the primary readout, comparison, normalisation and exclusion rule before the data exist.Experimental design & controls
- Pre-wetting
- Aspirating and dispensing the liquid two or three times with a new tip, to coat its wall and saturate the air cushion with vapour before the first real transfer.Pipetting & serial dilution
- Prey
- The protein (or library of proteins) fused to the activation domain, which must be recruited to the promoter to be seen.Yeast two-hybrid
- Primary / secondary antibody
- The primary binds the target; the labelled secondary binds the primary's constant region.Immunofluorescence
- Primary culture
- Cells grown directly from tissue, before the first passage; they have a finite lifespan and keep many tissue-specific properties.Primary cell isolation
- Primer dimer
- A short artefact (~40–60 bp) made when primers anneal to each other and get extended.PCR
- Primers annealing to each other and being extended. Short, melts low, invisible to a probe and fully visible to SYBR Green.Quantitative PCR (qPCR)
- Printability (Pr)
- L²/16A of a printed pore: 1 for a perfect square, lower when pores round off.Scaffold fabrication
- Probe
- A labelled single-stranded nucleic acid complementary to the sequence you want to detect; usually a few hundred bp to a kilobase, random-primed so it carries many labels.Southern blot
- A short labelled DNA or RNA containing the binding site, used at a concentration well below KD for affinity measurements.EMSA (gel shift)
- Probe-level summarisation
- Combining the several probes of a probe set into one value (RMA, MAS5 and relatives), with its own background and normalisation assumptions.Expression microarrays
- Product purity
- The fraction of edited reads carrying the intended base rather than one of the other possible outcomes at that position.Base & prime editing
- Progress curve
- Product against time for one reaction. Straight at the start, bending as substrate is used, product accumulates or the enzyme loses activity.Enzyme activity assays
- Propeller effect
- Local rotation of a dye on a flexible linker, which keeps polarisation low even when the labelled molecule is bound.Fluorescence polarization
- Protease inhibitor cocktail
- A mixture covering the serine, cysteine, aspartic and metalloprotease classes. Several components hydrolyse in aqueous buffer within days, so it is added fresh to the volume being used.Cell lysis & protein extraction
- Protein A / protein G
- Bacterial proteins that bind the Fc region of IgG with different species and subclass preferences. Protein G binds mouse IgG1 well, where protein A is weak: a common reason an IP fails for no apparent reason.Immunoprecipitation
- Protein corona
- The layer of plasma proteins that adsorbs on a particle in blood and determines much of its fate.Nanoparticle formulation
- Protein group
- A set of protein entries that the identified peptides cannot distinguish between. Reported as one row, which is why isoform claims need checking.Mass spectrometry proteomics
- Proteinase K
- A robust serine protease active in detergent and at 56 °C. It digests nucleases and the protein bound to DNA, and is itself inactivated later by the chaotrope or by heat.Genomic DNA extraction
- Protein-conjugate analysis
- Using UV and RI together, with each component's extinction coefficient and dn/dc, to split the mass of a glycoprotein or protein–detergent complex into protein and modifier.SEC-MALS
- Proteoform
- One specific molecular form of a protein from a given gene, including its modifications and processing. The horizontal train on a 2D gel is a proteoform series.2D gel electrophoresis
- A specific molecular form of a protein, with a defined set of modifications on the same chain. Bottom-up workflows average over proteoforms; they do not resolve them.Post-translational modification analysis
- Proximity extension assay (PEA)
- A format in which antibody-linked DNA oligos must both bind the same molecule before they can be extended and amplified, so cross-reactive antibody pairs produce no signal.Multiplex immunoassays
- Proximity ligation
- Ligation of connector oligonucleotides into a circle, which is only possible when two probes are within about 40 nm of each other.Proximity ligation assay
- P(s) curve
- Contact probability against genomic distance; its slope summarises chromatin compaction.3D genome mapping
- Pseudoreplication
- Counting sub-samples of one unit as independent replicates. It shrinks the error bars and inflates the degrees of freedom without adding information.Experimental design & controls
- Pseudotransduction
- Apparent expression from protein or RNA carried inside the vector preparation, which fades over the first two to three days.Viral transduction
- Pseudotyping
- Putting a different envelope protein (usually VSV-G) on the particle to change its tropism and let it be concentrated by ultracentrifugation.Viral transduction
- P-site offset
- The distance from a footprint's 5′ end to the codon in the ribosome's P site, used to place each footprint on a codon.Specialized RNA sequencing
- PTH-amino acid
- The phenylthiohydantoin derivative of the released residue, identified by its HPLC retention time against a standard mixture.Edman degradation
- Pulse labelling
- Exposing cells to a nucleotide analogue for a defined, short time so that only cells synthesising DNA in that window incorporate it.Proliferation & cell cycle
- PVDF electroblot
- Protein transferred from an SDS-PAGE gel onto polyvinylidene difluoride, the standard support for sequencing a single band. Transfer in an amine-free buffer such as CAPS.Edman degradation
- Pyroglutamate aminopeptidase
- The enzyme that removes an N-terminal pyroglutamate, exposing residue 2 for sequencing. It does nothing for acetylated N-termini.Edman degradation
Q
- q (Å⁻¹)
- Scattering vector, 4π sin θ / λ; small q corresponds to large distances in the particle.Small-angle X-ray scattering
- Quadrant streak
- A streak in three or four sections, sterilising the loop between them, so each section is a further dilution of the one before.Plating & streaking
- Quality value (QV)
- Phred-scaled confidence in a base call: QV = −10·log10(error probability).Sanger sequencing
- Quality-control strain
- A reference strain (such as E. coli ATCC 25922) tested in every run; its MIC or zone must fall in a published range for the run to be valid.Antimicrobial susceptibility (MIC)
- Quality-control strains
- Reference organisms with known reactions streaked on each new batch of medium to prove it selects and differentiates as it should.Selective & differential media
- Quenching
- Stopping the reaction at the end of the window: cold washes for the ligases, ascorbate, Trolox and azide for APEX2.Proximity labelling
- Loss of fluorescence through contact with, or energy transfer to, nearby groups such as disulfides, protonated histidines or the peptide backbone.Intrinsic fluorescence
- QV20+ length
- The number of bases in a read called at QV20 or better; the usual summary of read quality.Sanger sequencing
R
- R2 and linewidth
- Transverse relaxation rate; the linewidth in Hz is about R2/π.NMR spectroscopy
- Radius of gyration (Rg)
- Root-mean-square distance of the particle's scattering mass from its centre.Small-angle X-ray scattering
- From the angular dependence of the scattering, measurable only for particles above roughly 10 nm with visible light.SEC-MALS
- Raman band
- Inelastic scattering from water at a fixed energy shift from the excitation; a sharp band that moves with the excitation wavelength, not with the protein.Intrinsic fluorescence
- Random error (imprecision)
- The scatter of repeated dispenses, usually quoted as a CV. Adds in quadrature, so it grows as the square root of the number of steps.Pipetting & serial dilution
- Random hexamers
- A mixture of all 4096 six-base sequences, annealed cold. Primes any RNA at many points, giving flat coverage and short cDNA.Reverse transcription
- Randomised block
- Allocation in which every block (plate, day, cage, litter) contains all treatments, with the order randomised inside the block.Experimental design & controls
- Rare codon
- A codon the host decodes with a scarce tRNA, so ribosomes pause there and can drop off.Recombinant expression
- Rarefaction curve
- Features observed against reads sampled; a flattening curve means the sample has been sequenced deeply enough.Amplicon & microbiome sequencing
- Rate-zonal
- A gradient run stopped while bands are still migrating, so position reports sedimentation rate (size and shape).Centrifugation
- Rate-zonal separation
- Separation by sedimentation rate down a gradient, stopped before anything reaches equilibrium. Position depends on size as well as density, so the run time matters.Subcellular fractionation
- Ratio compression
- The shrinking of measured fold changes in isobaric labelling, caused by co-isolated peptides contributing their own reporter ions.Mass spectrometry proteomics
- Rayleigh range
- The distance from the sheet's waist over which its thickness grows by √2; it sets the usable field for a given thickness.Light-sheet microscopy
- Rayleigh ratio
- The normalised intensity of light scattered at an angle; the excess over the solvent is what MALS measures.SEC-MALS
- RCF (× g)
- Relative centrifugal field: the outward acceleration as a multiple of gravity, 1.118e-5 × r(cm) × rpm². The quantity that transfers between rotors.Centrifugation
- Read N50
- The length such that half of all sequenced bases are in reads at least that long.Long-read sequencing
- Read-share CV
- Coefficient of variation of the fraction of reads per sample; a common measure of pool balance.Library QC & pooling
- Recall and precision
- Share of true variants that were called, and share of calls that are true, measured against a truth set.Whole-genome sequencing
- Reciprocal co-IP
- Pulling the candidate partner and blotting for the original bait. A different antibody and a different epitope, so it fails in different ways.Immunoprecipitation
- Recognition site
- The short sequence an enzyme binds, usually 4–8 bp and often palindromic.Restriction digestion
- Recombineering
- Recombination-mediated genetic engineering: using phage recombinases (λ Red, or RecET) so that linear DNA with short homology arms recombines with the chromosome.Microbial genetics
- Reconciliation
- Checking a physical box against the inventory, tube by tube, and resolving every difference.Record keeping & sample tracking
- Red shift
- Movement of the emission to longer wavelengths, as when a buried tryptophan becomes exposed to water on unfolding.Intrinsic fluorescence
- Redox mediator
- A small, diffusing molecule that shuttles electrons between an enzyme label and the electrode.Biosensors
- Reducing vs non-reducing
- Whether DTT or 2-mercaptoethanol was added. Only the comparison of the two lanes identifies a disulphide-linked species.SDS-PAGE
- Reference channel
- An otherwise identical sensing channel without the recognition layer, subtracted to remove bulk and drift.Biosensors
- Reference set
- A collection of proteins of known structure whose CD spectra are used to deconvolute a new spectrum, as in CONTIN, SELCON, CDSSTR or BeStSel.Circular dichroism
- Refractive-index matching
- Imaging the cleared sample in a medium of the same index (RIMS ≈ 1.46, DBE ≈ 1.56), without which it turns turbid again.Light-sheet microscopy
- Refractive-index mismatch
- A difference between immersion medium and sample index that causes depth-dependent aberration and axial distortion.Confocal microscopy
- Refractory-period violation
- An inter-spike interval shorter than about 2 ms within a sorted unit: evidence of contamination.Extracellular recording
- Regressive staining
- Deliberate overstaining followed by removal of the excess with a differentiator.H&E staining
- Repetitive yield
- The fraction of signal kept from one cycle to the next, typically 90 to 95%. Fitted from the slope of a log plot of called residue against cycle.Edman degradation
- Replica plating
- Transferring the pattern of colonies on a master plate to other plates with sterile velvet, to find colonies that fail to grow under a selective condition.Plating & streaking
- Replication-competent lentivirus (RCL)
- A recombinant able to replicate; the contaminant that split packaging systems and self-inactivating LTRs are designed to prevent, and that clinical preparations are tested for.Viral transduction
- Reporter strain
- A yeast strain with its own GAL4 and GAL80 deleted, auxotrophic for histidine (and often adenine), carrying reporters behind GAL4 binding sites.Yeast two-hybrid
- Rescan
- A second heating of the same sample after cooling in the cell; the standard test of reversibility.Differential scanning calorimetry
- Rescue construct
- A target coding sequence altered or truncated so the duplex cannot bind it, expressed to test whether a phenotype is on-target.RNA interference
- Resin capacity
- How much fusion protein a given bead volume can hold. Offering more than the capacity leaves free bait in solution rather than adding sites.Pull-down assays
- Resolution (Å)
- The smallest lattice spacing for which meaningful intensities were measured. Lower numbers mean finer detail.X-ray crystallography
- Resolution (Rs)
- Peak separation divided by the sum of the peak widths; around 1.5 is where two peaks can be cut apart cleanly.Chromatography polishing
- Response element
- A short DNA sequence bound by a specific transcription factor, often repeated in tandem in front of a minimal promoter.Reporter assays
- Response factor
- How much signal a given protein produces per microgram relative to the standard. Bradford response factors vary about twofold between common proteins; copper-assay ones much less.Protein quantification
- Reverse pipetting
- Aspirating more than the set volume and dispensing only to the first stop, so the volume delivered is the piston stroke and the retained film is discarded.Pipetting & serial dilution
- Reverse transfection
- Adding complexes to the plate and then seeding cells into them, rather than onto an attached monolayer.Transfection
- Rf (relative migration)
- Distance a band travelled divided by the distance the dye front travelled. The quantity a gel actually measures; masses are read from it against a marker.SDS-PAGE
- RFLP
- Restriction fragment length polymorphism: a variant that creates or destroys a restriction site, read as a change in fragment sizes after digesting a PCR product.Genotyping
- RFU / RLU
- Relative fluorescence or luminescence units: instrument-specific arbitrary numbers that depend on gain, optics, plate and volume. Only meaningful against something measured on the same plate.Plate readers & fluorometry
- Rheobase
- The smallest sustained current that makes a neuron fire.Patch clamp
- Ribonucleoprotein (RNP)
- Cas9 protein pre-mixed with its guide, delivered directly; it acts within hours and is degraded quickly.CRISPR-Cas9 editing
- Richardson–Lucy
- An iterative maximum-likelihood deconvolution for Poisson noise; more iterations sharpen more and amplify noise more.Image analysis
- RIN
- RNA Integrity Number: a 1–10 score computed by an algorithm from the whole electropherogram, including the region between the peaks, trained against expert rankings of real traces. The number sequencing facilities specify.RNA integrity check
- RIN / DV200
- RNA integrity number (1–10, from the electrophoretic trace) and the percentage of RNA fragments above 200 nt, the metric used for FFPE samples.RNA-seq
- RIP (RNA immunoprecipitation)
- Immunoprecipitation of an RNA-binding protein from a native lysate, followed by identification of the associated RNAs by qPCR, array or sequencing.RIP & CLIP
- RIPA buffer
- A mixed-detergent lysis buffer (typically 1% NP-40, 0.5% sodium deoxycholate and 0.1% SDS in Tris-buffered saline) that extracts nearly all cell protein but disassembles most complexes.Cell lysis & protein extraction
- Risk assessment
- The written document that identifies hazards and sets the controls, containment, waste route and emergency plan before work starts.Lab safety & biosafety
- RLU
- Relative light units: luminometer counts, comparable only within one instrument and setting.Reporter assays
- Rmax
- Maximum response if every ligand site is occupied; scales with ligand density and analyte/ligand mass ratio.SPR & BLI
- rmax / rmin
- The radius of the bottom and the top of the liquid column. Force is quoted at rmax; the path length between them sets the run time.Centrifugation
- RNA integrity number (RIN)
- A 1–10 score of RNA degradation; above about 7 is usually needed for expression work.Tissue & blood collection
- RNase-free
- Not sterile and not autoclaved: RNase A survives autoclaving. It means certified reagents and consumables, kept for RNA work only, handled with gloves. Water and plasticware are treated with DEPC or supplied certified; glassware is baked.RNA extraction
- ROCK inhibitor
- A drug such as Y-27632 that blocks Rho-associated kinase and prevents the apoptosis of dissociated human pluripotent cells.Stem cell culture
- Rotational correlation time
- The characteristic time for a molecule to tumble, which grows roughly with its volume; compared with the fluorescence lifetime it sets the polarisation.Fluorescence polarization
- R-spondin
- A secreted protein that binds LGR4/5 receptors and enhances Wnt signalling, required to maintain intestinal stem cells in culture.3D culture & organoids
- RT efficiency
- The fraction of RNA copies converted to cDNA. Unmeasured in a normal experiment, variable between samples, and multiplicative across every transcript in a given reaction.RT-qPCR
- rtTA / TRE
- The reverse tet transactivator and the tetracycline response element it binds in the presence of doxycycline: the Tet-On pair.Stable cell line generation
- Rwork / Rfree
- Disagreement between observed and model amplitudes, for the reflections used in refinement and for a 5% test set that never was.X-ray crystallography
S
- Salting out
- Precipitating protein by adding a high concentration of a kosmotropic salt, which competes for the water that keeps the protein soluble. It does not denature.Precipitation
- Sanger decomposition
- Fitting the mixed sequencing trace of an edited pool (TIDE, ICE) to estimate each indel's frequency.CRISPR-Cas9 editing
- Satellite colonies
- Small colonies growing in the zone around a large colony where it has used up or destroyed an inhibitor; common round ampicillin-resistant colonies on old plates.Plating & streaking
- Small plasmid-free colonies growing where a resistant colony has destroyed the ampicillin around it.Liquid culture & strain storage
- Satellite colony
- A tiny untransformed colony growing in the halo of cleared ampicillin around a resistant colony. Not a transformant, and not pickable.Bacterial transformation
- Saturation
- Clipping of the tallest peak when too much sample is loaded. It lowers the apparent ratio and the score without anything being wrong with the RNA, and is the first thing to rule out when a good prep suddenly scores badly.RNA integrity check
- A band at the detector's ceiling. Every ratio involving it is compressed towards 1, so a measured fold change is a lower bound.Western blot
- Pixels at the camera's maximum value; their true intensity is unknown.Immunofluorescence
- Pixels at the detector's maximum; their true intensity is unknown.Gel & blot imaging
- Pixels at the camera's maximum count, where signal no longer rises with light.In vivo imaging
- Saturation (% sat)
- Ammonium sulfate concentration expressed as a percentage of saturation at that temperature, which is how recipes and nomograms are written.Precipitation
- Scanner ceiling
- The top of the detector's digital range, usually 65,535 counts. A clipped spot reports that number whatever is on it.Expression microarrays
- Scar
- Sequence left at a junction by the cloning method itself rather than chosen by the designer.Seamless assembly
- Scattering length
- The distance over which light loses about two thirds of its unscattered photons; ~50–100 µm for visible light and ~150–200 µm near 920 nm in brain.Confocal microscopy
- Schiff reagent
- Basic fuchsin decolourised with sulphurous acid; turns magenta when it reacts with aldehydes.Special stains
- SD test
- A control in which samples are denatured with SDS and heat before measurement, to tell a ligand-induced fluorescence change from a loss of protein.Microscale thermophoresis
- Secondary necrosis
- Loss of membrane integrity by apoptotic cells that are not cleared, as happens in culture.Apoptosis assays
- Secondary-only control
- Sample processed without primary; reveals non-specific secondary binding.Immunofluorescence
- Second-site mutation
- An unintended polymerase error elsewhere in the amplified DNA. Invisible unless you sequence the whole amplified region.Site-directed mutagenesis
- SEC-SAXS
- Measuring SAXS continuously as the sample elutes from a size-exclusion column, so each peak is measured free of aggregates.Small-angle X-ray scattering
- Sedimentation coefficient (s, s20,w)
- Velocity per unit centrifugal field, in svedbergs; s20,w is corrected to water at 20 °C so values compare between buffers.Analytical ultracentrifugation
- Sedimentation coefficient (s, svedberg)
- A particle's sedimentation velocity per unit field, in units of 10⁻¹³ s. A property of the particle, so 80S means the same thing in any rotor.Centrifugation
- Seeding efficiency
- Cells attached in the scaffold after seeding divided by cells seeded, best measured by DNA in the scaffold.Cell seeding on scaffolds
- Segregational loss
- Plasmid lost at division when there is no active partition system, typically a fraction of a per cent per generation.Synthetic gene circuits
- Selection
- An antibiotic or other condition in the medium that only plasmid- or marker-carrying cells survive.Liquid culture & strain storage
- Selection marker
- A resistance gene (puromycin, neomycin/G418, hygromycin, blasticidin) carried on the construct, or a fluorescent protein used for sorting instead.Stable cell line generation
- Selection stringency
- How hard a selection is set, best expressed as a fold over what the current population can already do.Directed evolution
- Selective medium
- A medium with an agent that suppresses part of the microbial population, such as bile salts, crystal violet, high salt or an antibiotic.Selective & differential media
- Self-assembled monolayer
- An ordered layer of thiols or silanes used to attach recognition molecules and block the surface.Biosensors
- Self-inactivating (SIN) vector
- A design with the promoter-enhancer deleted from the 3′ LTR, so the integrated provirus has no active LTR promoter.Viral transduction
- Self-ligation (recircularisation)
- A cut vector closing on itself. Its two ends start in the same molecule, so it is the ligation's main competitor.Ligation-based cloning
- Sendai virus vector
- An RNA virus vector that expresses reprogramming factors in the cytoplasm without integrating, and is gradually lost as cells divide.Stem cell culture
- Sense / scrambled probe
- A control probe with the same label and physical properties that cannot hybridise to the target; its signal is background by definition.In situ hybridization
- Sensitised emission
- Acceptor fluorescence caused by energy transfer from an excited donor, measured in the FRET channel after correcting for bleed-through and direct excitation.FRET, FRAP & FLIM
- Sequencing saturation
- The fraction of reads that are duplicates of molecules already seen; once it is high, deeper sequencing adds no new molecules.Spatial transcriptomics
- The share of reads that come from a molecule already seen; high saturation means more reads add few new UMIs.Single-cell RNA-seq
- Series-resistance compensation
- Electronics that add back the voltage lost across the access resistance.Patch clamp
- Serum lot testing
- Comparing growth (and assay behaviour) on a new serum lot against the current one before switching.Media & supplements
- Serum vs plasma
- Serum is the fluid after clotting; plasma is from anticoagulated blood and still contains clotting factors.Tissue & blood collection
- Sharps
- Anything that can cut or puncture; contaminated sharps are the main injury route in a biology lab.Lab safety & biosafety
- Shear thinning
- Viscosity falling as shear rate rises, which lets an ink flow through a needle and then hold its shape.Scaffold fabrication
- Viscosity falling as shear rate rises; the opposite is shear thickening.Rheology
- Shifted band
- The slower band of probe held in a protein complex.EMSA (gel shift)
- Short tandem repeat (STR)
- A locus of 2–6 bp repeats whose length varies between people; the basis of human cell line authentication.Contamination control
- shRNA
- A short hairpin RNA transcribed in the cell from a plasmid or integrated vector, processed to a duplex before loading. The way to make a knockdown last.RNA interference
- Sialomucin / sulphomucin
- Acidic mucins whose charge comes from sialic acid carboxyls or from sulphate esters.Special stains
- Sieving coefficient
- The ratio of a solute's concentration in the permeate to its concentration in the retentate. Zero is perfect retention; one is free passage.Dialysis & buffer exchange
- Concentration in the permeate divided by that in the retentate; near 0 for a retained product, near 1 for salts.Downstream processing
- Signal-to-background
- Band density divided by the membrane background next to it. It peaks at an intermediate antibody dilution, not at the highest.Western blot
- Silanisation
- Coating the master with a fluorosilane so cured PDMS releases cleanly.Microfluidic fabrication
- Silanol
- Surface Si–OH groups on glass and oxidised PDMS, the anchor points for silanes and the source of hydrophilicity.Surface modification
- Silent diagnostic change
- A second base change that does not alter the protein but creates or destroys a restriction site, so clones can be screened by digest before sequencing.Site-directed mutagenesis
- Single-molecule readout
- Each spot is one ligation event, so the assay counts events rather than measuring an intensity, and is limited by counting statistics.Proximity ligation assay
- Sink conditions
- A release medium kept well below saturation, conventionally under about a third of the drug's solubility, so the bath never limits release.Release & degradation studies
- siRNA
- A synthetic double-stranded RNA, usually 21 nucleotides with 2-nucleotide 3′ overhangs, that enters RISC directly without needing Dicer.RNA interference
- Site-determining ion
- A fragment ion produced by cleavage between two candidate residues, so its mass differs depending on which one carries the modification. Without one, the site is ambiguous.Post-translational modification analysis
- Site-localisation probability
- The confidence that the modification sits on one particular residue rather than another candidate in the same peptide. Separate from the confidence that the peptide was identified at all.Post-translational modification analysis
- Size adjustment
- Multiplying a qPCR result by standard size ÷ library size to correct for dye signal per molecule.Library QC & pooling
- Size factor
- A per-sample scaling that puts libraries of different depth and composition on a common scale before testing.RNA-seq
- A per-sample scaling for sequencing depth and composition, used to compare counts between samples.Read processing & analysis
- Sizing ladder
- The calibration run alongside the samples that converts migration time into size. Without it the instrument cannot place the integration windows or assign a score, so the trace becomes a picture rather than a measurement.RNA integrity check
- Skipped well
- A clear well between wells that grew at lower and higher concentrations; a sign of a pipetting error or contamination.Antimicrobial susceptibility (MIC)
- Small RNA cut-off
- The size below which a silica membrane stops retaining RNA, set by the ethanol fraction in the binding mix. Around 35% ethanol the cut-off is near 200 nucleotides; raising the ethanol to 50–65% brings tRNA, 5S and miRNA onto the column.RNA extraction
- Smear
- Continuous signal down a lane: degraded DNA, overloading or a mix of many sizes.Agarose gel electrophoresis
- A thin film of cells spread on a slide, dried and fixed before staining; it should look like a faint haze, not a cloud.Gram staining
- SMRTbell
- A circular template made by ligating hairpin adapters to both ends of a double-stranded insert.Long-read sequencing
- Snap freezing
- Freezing in seconds, usually in isopentane chilled by liquid nitrogen, to keep ice crystals small.Fixation & processing
- Snap-cool
- Chilling the denatured RNA–primer mix on ice so the primer anneals before the RNA refolds into the structure you just melted.Reverse transcription
- Soft-clipping
- Leaving the ends of a read unaligned while aligning the rest.Read processing & analysis
- Solubility tag
- A fusion partner (SUMO, MBP, thioredoxin, GST) that keeps the nascent chain soluble and is cleaved off afterwards.Recombinant expression
- Spacer
- The base pairs between the two half-sites. About 5–7 bp for zinc-finger nucleases and 12–21 bp for TALENs; outside that range no active dimer forms.Other editing & transgenesis
- Spanning read
- A read that covers a feature and anchors in unique sequence on both sides; needed to size repeats and resolve structural variants.Long-read sequencing
- Spatial barcode
- A sequence unique to one position on a capture array, added to every transcript caught there, so a read can be traced back to a place.Spatial transcriptomics
- Specific activity
- How much label a probe carries per unit mass. Along with the amount of RNA loaded, it sets the detection limit of a method with no amplification step.Northern blot
- Label per unit mass of probe, set by how much labelled nucleotide was included relative to its unlabelled counterpart.In vitro transcription
- Initial rate per mass of protein, usually µmol/min/mg. The standard unit for following a purification.Enzyme activity assays
- Specific competitor
- Unlabelled probe with the binding site; it removes the shifted band if the binding is specific.EMSA (gel shift)
- Specific growth rate (μ)
- Rate of biomass increase per unit biomass, per hour; ln 2 divided by the doubling time.Fermentation
- Specific lysis
- (Measured target death − spontaneous death) / (100% − spontaneous death): killing attributable to the effectors.Co-culture
- Specific productivity
- Product made per cell per unit time; distinct from titer, which also depends on how many cells there are and how long they live.Recombinant expression
- Spectral centre of mass
- The intensity-weighted mean emission wavelength; a smoother, more nearly linear measure than the peak position.Intrinsic fluorescence
- Spheroid
- A roughly spherical aggregate of cells grown without attachment to a surface; widely used as a simple 3D tumour model.3D culture & organoids
- Spike sorting
- Assigning detected spikes to individual neurons by waveform shape.Extracellular recording
- Spinning-disk crosstalk
- Out-of-focus light from a thick sample passing through neighbouring pinholes on the disk.Confocal microscopy
- Splice switching
- Using a steric-block oligo to change which exons are included in the mature message, the mechanism behind nusinersen and the exon-skipping oligos for Duchenne muscular dystrophy.Antisense oligonucleotides
- Spliced alignment
- An RNA-seq read split across an intron, with each part on its own exon.Read processing & analysis
- Splinted wound model
- A rodent excisional wound held open by a sutured ring so that it heals by re-epithelialisation rather than contraction.Disease & implant models
- Split proximity labelling
- An enzyme divided into two inactive halves on two baits, which only labels where the two baits meet: a way of mapping the neighbourhood of a specific complex rather than of one protein.Proximity labelling
- Split ratio
- The dilution applied at a passage, written 1:N: one part of the harvested cells goes into N parts of new culture.Aseptic technique & passaging
- Spontaneous and maximum release
- LDH in the medium of untreated wells, and in wells lysed with detergent; the 0% and 100% of an LDH assay.Viability & cytotoxicity
- Spot assay
- Strains normalised to the same density and spotted as a ten-fold dilution series on selective and non-selective plates, so growth can be compared row to row.Yeast two-hybrid
- Spot calling
- Deciding which intensity maxima in an image are single molecules, usually by a threshold expressed in multiples of the local background standard deviation.In situ hybridization
- Spread plate
- A known volume (usually 50–200 µL) of a dilution spread over the surface of a dried plate with a sterile spreader or glass beads.Plating & streaking
- SPRI beads
- Carboxyl-coated magnetic beads that bind DNA in PEG and salt; the bead-to-sample ratio sets the size cut-off.Library construction
- Sputter coating
- Depositing a few nanometres of metal on an SEM specimen to make it conductive.TEM & SEM
- A few nanometres of gold, platinum or carbon deposited on an insulating sample so it does not charge in the SEM.Material characterization
- SSC
- Saline–sodium citrate, the standard hybridisation and wash buffer. Concentrations are quoted as multiples of the 1× stock (0.15 M NaCl, 15 mM sodium citrate).Southern blot
- Stacking
- Concentration of the sample into a very thin disc at the gel interface before separation begins. It is what makes a sharp band possible.SDS-PAGE
- Stage-top incubator
- A heated, gassed and humidified chamber on the microscope stage that holds cells at 37 °C and 5% CO₂ during imaging.Live-cell & time-lapse
- Standard curve
- Cq against log input across a dilution series. Its slope gives amplification efficiency, its R² reports the dilutions, and its span is the assay's dynamic range.Quantitative PCR (qPCR)
- Absorbance measured for a dilution series of a protein of known concentration, used to convert a sample's absorbance into an equivalent mass of that standard protein.Protein quantification
- Signal for a dilution series of known concentrations, used to convert sample signal into concentration.ELISA
- Cq against log concentration for the standards; slope about −3.3 at 100% efficiency.Library QC & pooling
- Star activity
- Cutting at sequences that only resemble the recognition site, caused by wrong salt, excess glycerol, excess enzyme or very long incubation.Restriction digestion
- Static incubation
- Growth without shaking, so cells can settle and attach. Shaking the plate converts the assay into a (badly aerated) broth culture.Biofilm assays
- Stationary phase
- The plateau reached when a nutrient or oxygen runs out; cells change physiology and become more stress-resistant.Growth curves
- Steric block
- An oligo that cannot be cleaved and works by occupancy: masking a splice site, a splicing silencer, a start codon or a protein-binding site.Antisense oligonucleotides
- Sterilising-grade filter
- A membrane validated to retain at least 10⁷ Brevundimonas diminuta per cm² of membrane, in practice a 0.2 or 0.22 µm rating.Filtration & sterilization
- Sticky end
- A short single-stranded overhang left by an offset cut; two ends from the same enzyme are complementary and anneal.Restriction digestion
- Stimulated emission depletion
- Using a red-shifted beam to force excited molecules to emit at its wavelength, so only those at the doughnut's dark centre fluoresce normally.Super-resolution
- Stoichiometric staining
- Dye binding in proportion to DNA, which requires dye in excess over binding sites.Proliferation & cell cycle
- Stoichiometry
- The fraction of molecules modified at a given site.Specialized RNA sequencing
- Stoichiometry (n)
- Moles of ligand bound per mole of protein at saturation, taken from the midpoint of the isotherm; it also reports the active fraction of the protein.Isothermal titration calorimetry
- Stoichiometry (occupancy)
- The fraction of a protein's molecules carrying the modification at a given site. Rarely measured in discovery experiments and not what a fold change reports.Post-translational modification analysis
- Stokes shift
- The gap between a fluorophore's excitation and emission peaks. A large shift makes it easy to separate the two bands and keeps the background low.Plate readers & fluorometry
- Stokes–Einstein equation
- D = kT / (6πηRh), the link between diffusion coefficient and size, through temperature and solvent viscosity.Dynamic light scattering
- Stranded library
- A library that keeps the information about which DNA strand a transcript came from, usually by marking the second cDNA strand with dUTP.RNA-seq
- Stray light
- Light reaching the detector without passing through the sample. It puts a hard ceiling on absorbance and makes high readings come out low.UV-Vis spectrophotometry
- Streptavidin capture
- Pulling the biotinylated proteins out of an SDS lysate. The bond survives denaturants, so the washes can remove essentially everything that is not covalently labelled.Proximity labelling
- Streptolysin O
- An oxygen-labile haemolysin of Streptococcus pyogenes; it acts fully only below the surface or with reduced oxygen.Selective & differential media
- Stringency
- How much mismatch a hybridisation or wash tolerates, set together by salt concentration and temperature. Low salt and high temperature are stringent.Southern blot
- How close to perfectly complementary a duplex must be to survive hybridisation and washing; set by formamide, salt and temperature.In situ hybridization
- How hard the buffer and washes are on non-covalent binding. Raising it removes background and complexes at the same time, in that order.Immunoprecipitation
- Stripping and re-probing
- Removing the probe so the same membrane can be hybridised again, usually for a loading-control transcript. Each round costs some RNA.Northern blot
- Structure factor
- The modulation of the scattering by interactions between particles; equal to 1 in an ideal dilute solution.Small-angle X-ray scattering
- Stutter
- A minor PCR artefact one repeat shorter than the true allele, typically a few to ~10% of its height.Contamination control
- SU-8
- An epoxy-based negative photoresist that can be spun tens to hundreds of µm thick; exposed regions crosslink and remain.Microfluidic fabrication
- Sub-G1
- Events with less DNA than G1: debris and fragmented apoptotic nuclei.Proliferation & cell cycle
- Cells with less than G1 DNA content in a DNA histogram; fragmented apoptotic nuclei that have lost DNA.Apoptosis assays
- Substrate blank
- A well with substrate and everything except enzyme, at each substrate concentration, read through the same time course.Enzyme activity assays
- Substrate depletion
- Local exhaustion of ECL substrate over strong bands, so signal stops tracking protein amount.Gel & blot imaging
- Subtomogram averaging
- Aligning and averaging many copies of a structure extracted from tomograms.Cryo-EM
- Supercoiled
- The negatively supercoiled, covalently closed form native to a bacterial plasmid. It is compact, runs fast on a gel, and transfects better than relaxed or nicked DNA.Plasmid preparation
- Supercoiled DNA
- Twisted circular plasmid; runs faster than linear DNA of the same size.Agarose gel electrophoresis
- Supersaturation
- Protein concentration divided by its solubility under the drop's conditions. Crystals nucleate only when it is well above 1.X-ray crystallography
- Supershift
- A further reduction in mobility when an antibody binds the protein in the complex, identifying it.EMSA (gel shift)
- Surface erosion
- Degradation only at the surface, so mass and size fall steadily from the start.Material characterization
- Degradation confined to the outer layer, because hydrolysis outruns water penetration.Release & degradation studies
- Surface free energy
- The energy per area of a surface, split by Owens–Wendt into dispersive and polar components.Surface modification
- Switching buffer
- Oxygen-scavenging buffer with a thiol (e.g. MEA) that drives cyanine dyes into a reversible dark state so they blink.Super-resolution
- SYPRO Orange
- A dye whose fluorescence increases strongly in hydrophobic environments; supplied as a 5000× stock and used at about 2–10×.Thermal shift assays
- Systematic error (inaccuracy)
- The difference between the mean volume delivered and the volume set. Compounds down a dilution series and is invisible in replicates.Pipetting & serial dilution
T
- %T
- Total acrylamide concentration of the resolving gel. It sets the pore size and so the range of masses the gel resolves.SDS-PAGE
- TAD
- Topologically associating domain: a region whose loci contact each other more than they contact their neighbours.3D genome mapping
- TAE / TBE
- Running buffers. TAE suits large fragments and recovery; TBE gives sharper small bands and holds up in long runs.Agarose gel electrophoresis
- Take rate
- The fraction of injected animals in which a tumour establishes.Disease & implant models
- TALE repeat
- A ~34-amino-acid unit that reads a single base. One repeat per base, so a target needs no motif, but the arrays are highly repetitive to build.Other editing & transgenesis
- tan δ
- G″/G′. Below about 0.1 the material is solid-like; above 1 it flows.Rheology
- Tanabe score
- Percentage match between two STR profiles: 2 × shared alleles ÷ (alleles in query + reference).Contamination control
- Target engagement
- Evidence that a compound physically binds its intended target in the relevant setting, such as intact cells.Thermal shift assays
- Target retrieval
- Heating a fixed section in buffer to reverse part of the formalin cross-linking so a probe can reach the RNA.In situ hybridization
- Target-decoy search
- Searching spectra against a reversed or shuffled copy of the database alongside the real one, so the number of decoy matches above a score estimates the number of wrong real matches.Mass spectrometry proteomics
- Target-unrelated binder
- A clone selected for binding the plastic, the blocking agent, the capture reagent or the tag rather than the target.Phage & yeast display
- Taylor cone
- The conical meniscus at the needle tip from which an electrospinning jet is drawn.Scaffold fabrication
- TCSPC
- Time-correlated single photon counting: timing individual photons relative to laser pulses to build decay curves.FRET, FRAP & FLIM
- Technical replicate merging
- Combining the partitions of several wells into one measurement, which is how you get more molecules through a fixed-capacity instrument.Digital PCR
- Technical vs biological replicate
- Several wells of one cDNA versus independent samples each taken through extraction and RT. Only the second supports a biological claim.RT-qPCR
- TEER
- Transepithelial electrical resistance: (measured resistance − blank) × membrane area, in Ω·cm²; rises as tight junctions form.Co-culture
- Transepithelial (or endothelial) electrical resistance across a cell layer, blanked and normalised to area, in Ω·cm².Organ-on-chip
- Temperature jump (T-jump)
- The fast fluorescence change within the first second of heating, caused by the dye's own temperature dependence rather than by movement.Microscale thermophoresis
- Template switching
- The reverse transcriptase adds a few cytosines at the end of the cDNA, where an oligo anneals so full-length cDNA can be amplified (Smart-seq).Single-cell RNA-seq
- Reverse transcriptase adds untemplated cytosines at the 5′ end of the RNA, where an oligo anneals so the full cDNA carries an adapter at both ends.Specialized RNA sequencing
- TFZ and LLG
- Translation-function Z-score and log-likelihood gain from a molecular-replacement search; TFZ above 8 is usually an unambiguous solution.X-ray crystallography
- Thaw-mounting
- Touching a room-temperature slide to a frozen section so that it melts onto and sticks to the glass.Sectioning
- Therapeutic window
- The gap between the concentration at which the oligo is active and the concentration at which its chemistry is toxic. The number that decides whether a design is worth pursuing.Antisense oligonucleotides
- Thermophoresis
- Directed movement of molecules in a temperature gradient, sensitive to size, charge and hydration shell.Microscale thermophoresis
- Thermostable RT
- An engineered M-MLV variant that works at 50–60 °C, where RNA secondary structure melts; usually RNase H-minus as well.Reverse transcription
- Thin-film hydration
- Drying lipid from organic solvent and hydrating it above the transition temperature to form multilamellar vesicles.Nanoparticle formulation
- Thixotropy
- Structure that breaks down under shear and rebuilds over time at rest.Rheology
- Three-primer PCR
- One common primer with an allele-specific primer for each allele, giving products of different sizes in one tube.Animal genotyping
- Threshold
- The fluorescence level whose crossing defines Cq. It must sit in the log-linear phase, above the noise and below the plateau, and be the same for every well compared.Quantitative PCR (qPCR)
- Throughput (Vmax)
- The volume a membrane will pass before the flux falls to nothing, quoted per unit area. It is the number that decides whether a unit is big enough.Filtration & sterilization
- Time constant
- The decay time of an electroporation pulse, read off the instrument. A salt-free sample in a 1 mm cuvette gives about 5 ms; a salty one drops to well under 1 ms and usually arcs.Bacterial transformation
- Time-invariant noise
- A fixed radial pattern in absorbance scans from windows and optics, removed algebraically during fitting.Analytical ultracentrifugation
- Tip speed
- Speed of the impeller tip, π·D·N; a common, if crude, measure of how hard a tank is stirred.Bioreactor culture
- Tissue clearing
- Removing lipids and matching the refractive index of what remains, so light passes through the tissue without scattering.Light-sheet microscopy
- Titer
- Product concentration in the harvest, usually mg/L: the number quoted for secreted expression.Recombinant expression
- Titration
- Testing antibody amounts to find the one with the best separation between positive and negative cells.Flow cytometry & FACS
- Testing a series of dilutions on control tissue to find the one that separates weak from strong without background.Immunohistochemistry
- Tm
- Melting temperature: the midpoint of a thermal unfolding transition, where half the protein is unfolded.Circular dichroism
- Tm (melting temperature)
- The temperature at which half of a primer is bound to its target. Annealing is set relative to it.PCR
- Tn5 transposase
- An enzyme that cuts DNA and inserts the adapters it carries in one step (tagmentation); in ATAC it only reaches accessible DNA.ATAC-seq
- Tn5 transposase (tagmentation)
- An enzyme that fragments DNA and inserts adapter sequences at the same time.Library construction
- Tokuyasu cryosection
- An ultrathin section cut from a sucrose-infused, frozen, lightly fixed sample, labelled after thawing.TEM & SEM
- Top-heavy read
- Very strong early peaks that fade quickly, the typical result of too much template.Sanger sequencing
- Topoisomerase cloning
- A vector supplied with topoisomerase I covalently attached to each end, so the energy for the bond is pre-stored and no ligase or ATP is needed.Ligation-based cloning
- Total flux
- Photons per second from a region of interest: the exposure-independent unit for bioluminescence.In vivo imaging
- Total-protein normalisation
- Correcting lane loading by a stain of all protein in each lane rather than by one housekeeping protein.Gel & blot imaging
- Tracer
- The small fluorescent ligand whose polarisation reports binding, used at a fixed low concentration.Fluorescence polarization
- Transcardial perfusion
- Flushing the circulation through the left ventricle, usually followed by fixative, under deep terminal anaesthesia.Tissue & blood collection
- Transcript size
- The length of the whole RNA, read by interpolating a band's position between ladder bands on a denaturing gel. Precise to a few per cent.Northern blot
- Transducing unit (TU)
- A particle that produces a scoreable event in the titration assay used; an operational unit, not a count of particles.Viral transduction
- Transfection efficiency
- The fraction of cells that take up the reagent. Low efficiency looks exactly like a weak duplex in a population measurement.RNA interference
- Transfer efficiency
- The fraction of a protein that leaves the gel and sticks to the membrane. Falls with size for a fixed transfer, and falls for small proteins when the transfer is long.Western blot
- Transfer function
- A module's steady-state output as a function of its input; its shape, not just its range, decides whether a design works.Synthetic gene circuits
- Transformation efficiency
- Colony-forming units per microgram of DNA, measured with a known supercoiled plasmid at an amount small enough that colonies still rise in proportion to DNA.Bacterial transformation
- Transient expression
- Expression from a plasmid that does not replicate or integrate, so it fades over days as the cells divide.Transfection
- Translation efficiency
- Footprint density on a coding sequence divided by its mRNA abundance.Specialized RNA sequencing
- Transmembrane pressure (TMP)
- The average pressure difference across a membrane between the feed side and the permeate side.Downstream processing
- Transwell insert
- A cup with a porous membrane floor that hangs in a well, creating apical and basolateral compartments that share medium through the pores.Co-culture
- TROSY
- An experiment that selects the slowest-relaxing component of the signal, which together with deuteration makes large proteins accessible.NMR spectroscopy
- Trypsin-EDTA
- Protease plus chelator used to detach adherent cells; neutralised by serum or a soybean trypsin inhibitor.Aseptic technique & passaging
- TSS enrichment
- Insertions at transcription start sites relative to the flanks 2 kb away; a measure of signal over background.ATAC-seq
- Tumour growth inhibition (TGI)
- How much smaller treated tumours are than vehicle tumours at a set time, usually compared on log volume.Disease & implant models
- Tumour purity
- Fraction of cells in a tumour sample that are cancer cells; it scales every somatic allele fraction.Whole-genome sequencing
- TUNEL
- Terminal deoxynucleotidyl transferase dUTP nick-end labelling of DNA strand breaks.Apoptosis assays
- Tunnel handling
- Moving mice with a tube or cupped hands instead of by the tail, which reduces anxiety.Handling & dosing
- Turbidity read-out
- Magnesium pyrophosphate, a by-product of nucleotide incorporation, precipitating enough to cloud the tube visibly.Isothermal amplification
- Two-photon excitation
- Simultaneous absorption of two infrared photons; it scales with intensity squared, so it only happens at the focus.Confocal microscopy
- Two-point calibration
- Setting a pH meter with two standards that bracket the pH you'll measure.Buffer & media preparation
- Type IIS enzyme
- A restriction enzyme that cuts a fixed distance outside its recognition sequence, so the site is removed from the product.Seamless assembly
U
- UGI
- Uracil glycosylase inhibitor, included in cytosine base editors to stop the cell excising the uracil intermediate before it is copied through.Base & prime editing
- Ultra-low-attachment (ULA) plate
- Plasticware with a hydrophilic, protein-repellent coating that prevents cells from attaching.3D culture & organoids
- UMI
- A random sequence on each primer that marks each captured molecule, so PCR copies are counted once.Single-cell RNA-seq
- UMI (unique molecular identifier)
- A short random barcode added to each original molecule so its reads can be grouped and collapsed into a consensus.Exome & targeted panels
- Unique dual indexes (UDI)
- Index pairs in which neither index is shared with another sample, so swapped (hopped) index reads can be discarded.Library construction
- Unit
- The amount of enzyme that digests 1 µg of a reference substrate in 1 hour under the supplier's conditions. It is a definition tied to that substrate, not a universal rate.Restriction digestion
- Unstirred layer
- The quiescent film of liquid against a membrane. It makes the local gradient much shallower than the bulk gradient, which is why dialysis buffer is stirred.Dialysis & buffer exchange
- Untemplated 3' A
- The single adenine Taq-type polymerases add to most product ends; the basis of TA cloning and absent from proofread products.Ligation-based cloning
V
- V₀ and Vt
- Void volume (where excluded molecules elute) and total column volume (where small molecules elute); everything separates in between.Chromatography polishing
- Valency
- Copies of the displayed fragment per particle; monovalent display reports single-interaction off-rates, polyvalent display reports avidity.Phage & yeast display
- Valid pair
- A read pair from a true ligation junction between two different fragments, after removing dangling ends, self-circles and duplicates.3D genome mapping
- Van 't Hoff enthalpy
- The unfolding enthalpy implied by the steepness of a two-state transition; it equals the calorimetric enthalpy only for a true two-state process.Circular dichroism
- Van 't Hoff enthalpy (ΔHvH)
- The enthalpy implied by the sharpness of the transition under a two-state model.Differential scanning calorimetry
- Variant allele fraction (VAF)
- Share of reads at a position that carry the alternative allele.Whole-genome sequencing
- Vector copy number (VCN)
- Integrated vector copies per genome, measured by qPCR or ddPCR against a single-copy reference.Viral transduction
- Vehicle
- The solvent a compound is delivered in. The comparison group gets it at the same final concentration and nothing else.Experimental design & controls
- Vehicle control
- Cells given the solvent alone at the same final concentration as the treated wells; the 100% reference.Viability & cytotoxicity
- Animals given the vehicle alone by the same route and handling, so the procedure's own effects can be separated from the compound's.Handling & dosing
- Viability
- Percentage of cells with intact membranes (unstained).Cell counting & viability
- Viability dye
- A dye that enters dead cells (with leaky membranes) so they can be gated out.Flow cytometry & FACS
- Viewpoint
- In 4C, the restriction fragment whose contacts are amplified by inverse PCR.3D genome mapping
- Viscoelasticity
- Combined elastic and viscous behaviour, so the response depends on loading rate and time.Tensile & compression testing
- Vitreous ice
- Amorphous, glass-like frozen water formed by cooling at around 10⁵ K/s or faster.Cryo-EM
- Vmax
- The throughput per filter area at which a filter would block completely; used to size depth and membrane filters.Downstream processing
- Void volume
- The liquid outside the beads of a size-exclusion bed. Fully excluded molecules elute in it; this is also what dilutes a desalted sample.Dialysis & buffer exchange
- Void volume (V₀)
- Where everything too large to enter the pores elutes; MALS still weighs what comes out there, so aggregates are quantified rather than lumped together.SEC-MALS
- Volt-hours (kVh)
- The integral of voltage over time, which is how the end of focusing is specified. Typically 40–60 kVh for an 18 cm strip.2D gel electrophoresis
- Volume ratio
- Buffer volume divided by sample volume. One change can at best leave 1/(1+ratio) of the solute behind.Dialysis & buffer exchange
- Vroman effect
- Exchange of adsorbed proteins over time, as abundant early proteins are displaced by ones with higher affinity.Surface modification
- vvm
- Gas flow in vessel volumes per minute.Bioreactor culture
W
- Wall shear stress
- The stress on cells at the needle wall, ΔP·R/2L, the main cause of cell death during extrusion.Scaffold fabrication
- Frictional force per area that flowing medium exerts on cells; 6μQ/(wh²) in a shallow channel, quoted in Pa or dyn/cm².Organ-on-chip
- Warm ischaemia time
- Time from loss of blood supply to stabilisation of a sample, during which it degrades.Tissue & blood collection
- Washout
- Loss of the culture from a chemostat when D exceeds the maximum growth rate.Fermentation
- Watershed / declumping
- Splitting touching objects along ridges between seed points, often seeds from distance-transform maxima.Image analysis
- Weaning
- Stepwise reduction of serum so that cells adapt to a serum-free medium over several passages.Media & supplements
- Weiss unit
- The historical unit of T4 ligase activity, defined by exchange of phosphate into ATP; suppliers also quote cohesive-end units, and 1 Weiss unit is roughly 60–70 of them.Ligation-based cloning
- Wet glass transition
- The glass transition temperature of the water-plasticised polymer, around 40 °C for PLGA; above it the matrix is rubbery.Release & degradation studies
- Whole-mount immunolabelling
- Staining an intact organ with antibodies, which must diffuse in over days to weeks.Light-sheet microscopy
- Wide-bore tip
- A pipette tip with the end cut off or moulded wide, used to reduce the shear rate at the orifice when moving long DNA.Genomic DNA extraction
- Wiener parameter
- The regularisation in SIM reconstruction: low values sharpen but amplify noise into artefacts; high values smooth.Super-resolution
- Working cell bank (WCB)
- A larger set of vials made from one MCB vial, used to start experiments.Cryopreservation & banking
- Working range
- The span of concentrations over which an assay's standard curve is usable. Samples outside it are diluted or concentrated, not extrapolated.Protein quantification
- Wound closure
- 1 − open area at time t ÷ open area at 0 h, for the same field.Migration & invasion
X
- Xenograft
- Tissue or cells from one species grown in another, typically human tumour cells in immunodeficient mice.Disease & implant models
Y
- Y-adapter
- A partly double-stranded adapter whose unpaired arms make the two ends of each library molecule different, so every insert can be read from both sides.Library construction
- Yield coefficient (Yx/s)
- Grams of biomass made per gram of substrate consumed; about 0.5 g/g for glucose respired by E. coli or yeast.Fermentation
- Yield stress
- Stress at which deformation stops being recoverable; for many polymers the peak before necking.Tensile & compression testing
- Young's modulus (E)
- Slope of stress against strain in the initial linear region; a measure of stiffness.Tensile & compression testing
Z
- Z′ factor
- A measure of screening assay quality from the window and the scatter of the positive and negative controls.Fluorescence polarization
- 1 − 3(σ₊ + σ₋)/|μ₊ − μ₋| for positive and negative controls; a measure of the assay window.Viability & cytotoxicity
- Assay-quality score from control wells: 1 − 3(σ₊ + σ₋)/|μ₊ − μ₋|; ≥ 0.5 separates hits well.Live-cell & time-lapse
- Zeta potential
- Electrokinetic potential at the slipping plane, measured from electrophoretic mobility; depends on the medium as much as on the particle.Nanoparticle formulation
- Z′-factor
- A measure of assay quality combining the separation of the positive and negative controls with their variability; above 0.5 is generally taken as screening-ready.Plate readers & fluorometry
- Zimm equation
- Relates the excess Rayleigh ratio to concentration, molar mass, Rg and the second virial coefficient; the basis of all static light-scattering mass determination.SEC-MALS
- ZMW (zero-mode waveguide)
- A nanowell small enough that only the polymerase at its floor is illuminated, so one molecule is watched at a time.Long-read sequencing
- Zonal fixation
- A well-fixed rim around a core that formalin did not fix in time, with visibly different morphology and staining.Fixation & processing
- z-stack
- A series of optical sections taken at regular focus steps, viewed as slices, side views or 3D renderings.Confocal microscopy
- Z-VAD-FMK
- A cell-permeant, irreversible pan-caspase inhibitor; the specificity control for caspase signals.Apoptosis assays
- z-value
- The temperature change that alters the D-value tenfold; 10 °C for moist heat, which is what makes 131 °C ten times as lethal as 121 °C.Filtration & sterilization