Biology laboratory technique

A method for manipulating or measuring a biological system. Its readout must be connected to the intended biological quantity through controls and assumptions, rather than treating the instrument’s signal as a complete mechanism.

Characterization of cells through detectable molecular markers, often using antibodies. Marker combinations can distinguish populations, but expression of one marker alone does not establish every aspect of cellular identity.

Use of dyes or related reagents to distinguish structures in biological material. Selective staining can reveal structures difficult to see directly, but preparation and reagent effects must be assessed.

A histological stain that detects certain carbohydrate-rich structures after chemical oxidation produces reactive groups. The staining pattern identifies chemical properties and location rather than a unique molecule.

Staining that identifies organisms or material retaining dye after an acid-containing decolorization step. The property reflects cell-envelope chemistry; a positive stain alone does not identify every species or demonstrate viability.

A dye used in tissue investigation, notably for detecting amyloid through characteristic staining and optical behavior. Dye binding supplies evidence about an ordered deposit rather than identifying the precursor protein by itself.

Selective destruction of cells to test their necessity or the response of surrounding tissues. Compensation and collateral injury complicate interpretation; ablation alone is not a record of ancestry.

A measured molecular feature used to identify a cell state, tissue or experimental condition. Marker loss can reflect altered expression without loss of the cells themselves.

Visualization of proteins through binding of a dye or another detectable label. Signal depends on the staining chemistry and response range, so equal visual darkness need not establish equal molar amounts of different proteins.

Detection of proteins with Coomassie dyes, commonly after electrophoresis. Binding produces visible bands whose intensity can support comparison under controlled conditions, with background and saturation limiting quantification.

Quantification of image darkness or signal intensity over a defined region. Background subtraction and a checked response range are necessary before using integrated signal as a proxy for molecular amount.

Detection of selected DNA fragments after electrophoretic separation and transfer to a blotting membrane, using a complementary probe. The membrane preserves a spatial pattern of fragments; matching probe signal supports a sequence relationship rather than proving that all similarly sized fragments are identical.

A blotting membrane is a thin support onto which separated biological molecules are transferred so they can be retained and probed. In a Southern blot, DNA fragments separated by gel electrophoresis keep their relative spatial pattern during transfer. A complementary labelled probe then detects fragments carrying a matching sequence. ^[ref]

The membrane and the probe do different jobs: the first immobilizes the sample pattern, while the second supplies sequence-selective detection. A signal at the same migration position establishes neither complete sequence identity nor equal copy number without appropriate controls. Transfer efficiency, sample loading and probe binding can all affect intensity. The support therefore turns a transient separation into a reusable surface for molecular recognition.

Localization of a nucleic acid sequence through hybridization of a labelled complementary probe. Controls for probe specificity, background and tissue preservation are required.

Labeling a cohort briefly and following its fate during an unlabeled chase; useful for separating transport kinetics from steady-state localization.

Placement of a graft in the corresponding anatomical organ or site. It preserves more relevant local context than some ectopic grafts but still bypasses natural tumour initiation.

A bacterial DNA-transposition enzyme adapted for adapter insertion in ATAC-seq. Accessibility and sequence-dependent insertion bias both influence recovered fragments.

Measurement of newly synthesized RNA to distinguish early transcriptional changes from accumulated RNA abundance. Short-interval perturbations help prioritize direct regulatory responses.

An assay in which a measurable output is linked to a chosen regulatory sequence or activity. Reporter RNA abundance, biological translation and protein stability can affect the same endpoint differently.

A short nucleic acid sequence used to recognize a complementary target by hybridization. Specificity depends on sequence and conditions, so a detected signal must be distinguished from binding to a related off-target sequence.

Detection of nucleic acid targets within cells or tissues using fluorescent probes. It connects sequence recognition with spatial position, while probe design and background affect which signal can be assigned to a target.

A measurement system that converts a biological or biochemical interaction into an observable signal.

A sensor designed to report an oxidation-reduction-sensitive variable. Localization, calibration, dynamic range and sensitivity to other conditions determine what its signal can establish.

Enrichment of chromatin associated with a selected protein, followed by measurement of the recovered DNA. Association with a fragment need not mean direct base-specific binding; sequential enrichment can test co-association while retaining those resolution limits.

Sequencing recovered DNA to map chromatin associated with a protein or modification. antibody specificity, fragment resolution and normalization constrain interpretation.

A dye-binding estimate of protein concentration using a calibration series and absorbance near $595\mathrm{nm}$. Protein-dependent dye response, buffer interference and blank treatment limit how directly a bovine serum albumin standard estimates another protein.

Microscopy of cells and tissues within a living organism, allowing direct observation of behaviour in a physiological setting subject to preparation and imaging constraints.

A graft transferred between species. Tumour xenografts test behaviour in the recipient setting, which may lack immune interactions present in the original host.

A graft derived from a patient tumour and propagated in another species. Engraftment and serial passage can select lineages and alter the representation of the original sample.

Isolation of a target through antibody binding and recovery of the resulting complex. Associated molecules can be recovered too, but co-isolation does not establish a direct physical contact between every pair.

Detection of individual RNA molecules by multiple sequence-complementary fluorescent probes. Probe specificity, molecule detection and compartment boundaries require validation before interpreting subcellular enrichment.

Identification of many nucleic acid targets through repeated rounds of fluorescent hybridization and imaging. Matching signals across rounds connects temporal coding with spatially retained molecular identities.

A highly multiplexed imaging approach extending sequential RNA hybridization through additional spatial and temporal coding. It connects repeated fluorescence measurements with transcriptome-scale identification while retaining positions in tissue.^[ref]

An RNA-imaging method using combinatorial codes with error-detection or correction properties. Redundant measurements help distinguish a true molecular identity from an imperfect sequence of observed signals.^[ref]

Sequencing of RNA fragments protected by ribosomes to measure their positions on transcripts. Occupancy measures a combination of entry, passage and dwell time; more footprints can reflect slower elongation rather than more completed protein.

Methods that preferentially capture ribosomes near biological translation starts, often using short inhibitor treatments. Candidate peaks require calibration and independent validation.

Frame-related enrichment at a three-base interval in correctly positioned translating-ribosome reads. It supports biological translation but is difficult to establish for very short or low-count reading frames.

An RNA fragment protected from digestion by a ribosome in the assayed preparation. Length, genomic position and frame periodicity help distinguish productive biological translation from other protected RNA.

Profiling of preserved ribosomal and small-subunit-associated complexes to distinguish stages including scanning and recycling. Captured distributions remain subject to crosslinking and fragment-selection biases.

Incorporation of a traceable precursor into newly synthesized RNA. A pulse and chase separates labelled-cohort survival from continuing synthesis, provided incorporation, chase efficiency, toxicity and reutilization are controlled.

Experimental inference of RNA secondary structure or accessibility from chemical or enzymatic reactivity. Changes in reactivity can also reflect protein shielding, so comparisons and orthogonal controls are necessary.

Recovery of an RNA-associated complex using an antibody against a chosen protein. The associated RNA need not contact that protein directly, especially when partners remain intact during isolation.

RNA immunoprecipitation followed by sequencing of recovered RNA. Enrichment suggests association with the selected protein complex under the assay conditions, not necessarily direct binding to every recovered transcript.

An engineered transcript containing a selected RNA splicing region in a controlled expression context. Mutating a candidate cis-regulatory element tests local function, but an isolated construct can omit distant regulation or native chromatin context.

Mapping close RNA–protein contacts by crosslinking, immunoprecipitation of a selected protein and analysis of attached RNA fragments. Input abundance, antibody specificity and crosslinking bias constrain the interpretation of an apparent binding peak.

Sequencing-based mapping after crosslinking and immunoprecipitation. Stabilizing RNA–protein contacts before isolation can improve positional evidence, while crosslinking and recovery biases affect which interactions are observed.

A crosslinking approach using photoactivatable nucleoside analogues to mark RNA–protein contacts. Characteristic sequence changes help localize contacts, connecting chemical labeling with transcriptome-wide binding maps.^[ref]

An enhanced crosslinking-and-immunoprecipitation method for mapping RNA-binding protein contacts. Its controls and library design improve interpretation of enriched sites, without making every recovered sequence a functional regulatory target.^[ref]

An individual-nucleotide-resolution crosslinking-and-immunoprecipitation method. Recovering information from reverse-transcription termination helps locate RNA–protein contacts, linking a biochemical event with a sequence position.^[ref]

Transfer of identified cells into a recipient environment to test survival, developmental potential and interactions. Appropriate graft controls distinguish environmental influence from injury.

Pulse-chase analysis marks a cohort during a short pulse, then follows it while unlabeled precursor reduces subsequent labeling during the chase. Label specificity and effective suppression of new incorporation constrain interpretation.

A cell retaining a dilution-sensitive label after a chase. Retention can reflect slow division, terminal differentiation or assay properties; it is not by itself a functional stem-cell test.

Autoradiography localizes a radioactive label through its effect on a recording medium. In electron microscopy, developed photographic grains are compared with specimen structures; their positions have finite localization precision.