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CRISPR-screening-vocabulary

This collection is inspired by awesome-single-cell / awesome-CRISPR / single-cell-vocabulary.

Terms

List of terms related to CRISPR screening, etc.

  • Forward genetics

    • Screening approach in which genes involved in the phenotype of interest are identified by screening genetically perturbed cells.

  • Pooled CRISPR screen

    • A technique in which genetically encoded perturbations are introduced in bulk and read out with sequencing or imaging technology.

  • Arrayed CRISPR screens

    • A technique in which perturbations are introduced in individual reaction compartments and remain physically separated.

  • High-content CRISPR screens

    • Screens combining complex models, perturbations and stimuli with data-rich read-outs.

  • Biological replicates

    • Separately conducted repetitions of the same CRISPR screen using cells from different individuals or different passages of a cell line

  • Coverage

    • The average number of cells per guide RNA (gRNA) in a CRISPR screen.

  • Multiplicity of infection (MOI)

    • The average number of virions (and, by extension, guide RNAs (gRNAs)) delivered per cell during infection.

  • Genetic interactions

    • The combined effect of the simultaneous perturbation of several genes, which may deviate from the sum of the individual effects.

  • Positive selection screens

    • Also known as enrichment screens. Cells with the phenotype of interest are selected (enriched) in the screens; other cells are depleted.

  • Negative selection screens

    • Also known as dropout screens. Cells with the phenotype of interest are depleted in the screen; other cells are maintained.

  • Effective dose

    • The intensity of a perturbation (such as a drug or virus) that causes an effect (such as cell death) in a specified percentage of cells.

  • Screening hits

    • Target genes identified as being associated with the phenotype of interest in a CRISPR screen.

  • scCRISPR-seq

    • An umbrella term for a group of methods that combine pooled CRISPR sequencing with a single-cell sequencing read-out.

  • Manifold learning

    • A set of machine learning methods that seek to uncover hidden structures in the data through dimensionality reduction.

  • Variants of uncertain significance

    • Genetic variants for which there is insufficient genetic evidence to support or exclude a causal phenotypic effect.

  • Saturation genome editing

    • Introduction of many genome edits into a gene or regulatory element, with the goal of comprehensively assessing their phenotypic impact.

  • Synthetic lethality

    • Special case of a genetic interaction in which knockouts of two genes are individually tolerated, but their combination is lethal to cells.

  • False positives

    • Putative CRISPR screening hits that do not validate, which can be caused by technical biases.

  • False negatives

    • Potential CRISPR screening hits that would have validated but were missed, which can be caused by suboptimal screening conditions.

  • Population bottlenecks

    • Reductions in the genetic diversity among a pool of cells owing to external events.

  • Genetic drift

    • Genetic changes over time in a pool of cells, caused by random and uncontrolled events.

  • Unique molecular identifiers

    • Short barcodes that uniquely identify individual DNA or RNA molecules.

References