TABLE 1.

Frequently used concepts in CRISPR screening.

Concept	Definition
Coverage	Average number of cells infected by each sgRNA or shRNA. Calculated by dividing the total number of cells by the total number of sgRNA or shRNA in the library. Example: “cells were propagated at a minimum coverage of 200x”
Sequencing depth	The number of next-generation sequencing (NGS) reads mapped to sgRNA or shRNA sequences
Recovery	The fraction of the library for which a sgRNA or shRNA is detected in the NGS data x number of times. Example: “80% of the library was recovered at least 5 times”
Log2 fold-change (Log2FC)	Change in abundance of individual sgRNA- or shRNA-infected cells, normalized for sequencing depth, between two conditions, Log2-transformed. Example: Log2FC of 3 = 8-fold increase in abundance
Z-score	Number of standard deviations below or above the mean of a given Log2FC in comparison to the distribution of all Log2FC values. It is often used to report the effect of perturbing individual genes by integrating the Log2FC values for all sequences targeting the gene
Dropout	Loss of representation of a sgRNA or shRNA among the library recovered by NGS, either due to a biological effect or stochasticity
Bottleneck effect	Random dropout of sgRNA- or shRNA- infected cells from a population due to sampling of a small number of cells, for example during passaging with high dilution