Files and data to accompany "Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations" published in eLife: CITE AS: eLife2022;11:e71809 DOI: https://doi.org/10.7554/eLife.71809
AML-ML-04092020-emp-v10.R: R-code to quantify the fitness costs of the four different transgenetic constructs from the observed frequency trajectories in our D. melanogaster cage populations. Uses functions implemented in AML-ML-v10.R.
AML-ML-09042021-sim-v10.R: R-code to simulate construct frequencies given different fitness cost estimates. Uses functions implemented in AML-ML-v10.R.
AML-ML-v10.R: R-code of previously developed maximum likelihood framework (https://doi.org/10.1534/genetics.118.301893) modified to model two unlinked autosomal loci, representing the construct and a single idealized off-target site.
gene_drive_off_target_effects.slim: Agent-based simulation framework implemented in SLiM3 to study the consequences of off-target fitness costs on the invasion potential of homing and suppression gene drives.
constructs.zip: annotated sequences of the final construct insertions in ApE format (http://biologylabs.utah.edu/jorgensen/wayned/ape).
data/: Data used by AML-ML-v10.R. FitnessModes.txt contains the tested models encoded as integer vectors; rawData/ contains the raw genotype counts of our D. melanogaster cage populations (can also be found in Supplemental_Data_Sets.xlsx); TransitionMatrix.txt contains expected offspring counts for each genotype combination.
example-pictures.zip: A picture sample set for the image-based screening pipeline (Macro-Feb2020-manualClassification.ijm).
Macro-Feb2020-manualClassification.ijm: Macro of the image-based screening pipeline.
phenotype_assays.zip: Raw data of the phenotypic assays. Used by Phenotypes.R.
Phenotypes.R: R-code to analyze the phenotypic assays.
Supplemental_Data_Sets.xlsx: Raw counts of each experimental population (different constructs and the Cas9HF1 homing drive).