Analysis Code for Manuscript "Comparative Optimization of Combinatorial CRISPR Screens".
Utility function and analysis pipeline are indexed R files above.
Figure/Table preparation code can be found in corresponding R files (As indicated in file name).
Please refer to below Figure Legend and table sheet for file look-up:
MAIN FIGURE LEGEND
- Fig 1: Comparison of combinatorial CRISPR libraries.
- Fig. 2: Performance of combinatorial systems at the single-gene knockout level.
- Fig. 3: Positional effects and recombination rate on gene targeting.
- Fig. 4: Benchmarking of dual-knockouts by pan-essential paralog pair.
- Fig. 5: Positive and negative regulators of the MAPK pathway exhibit synergistic dependencies in NRAS-mutant melanoma.
EXTENDED DATA FIGURE LEGEND
- Extended data Fig. 1: Composition of the combinatorial libraries.
- Extended data Fig. 2: Quality controls for combinatorial systems and the screen performance.
- Extended data Fig. 3: Evaluation of enCas12a and Cas9 sgRNA design.
- Extended data Fig. 4: Comparison of LFC of pan-essential paralog pairs.
SUPPLEMENTARY TABLE
- Supplementary table 1: List of pan-essential genes
- Supplementary table 2: List of non-essential genes
- Supplementary table 3: List of pan-essential pairs
- Supplementary table 4: List of non-essential pairs
- Supplementary table 4: List of non-essential pairs
- Supplementary table 5: Cas9 sgRNA sequences and source
- Supplementary table 6: Cas9 sgRNA pair combinations
- Supplementary table 7: Cas12a sgRNA and PFAM annotation
- Supplementary table 8: Cas12a sgRNA pair combinations
- Supplementary table 9: Raw counts from CRISPR screens
- Supplementary table 10: LFC from CRISPR screens
- Supplementary table 11: GEMINI sensitive synergy score from CRISPR screens
DATA AVAILABILITY
All sequencing data is deposited in SRA under project PRJNA792754.
The raw data for running the analysis pipeline can be found in this raw data dropbox folder and also in this Figshare link.
The intermediate/processed data for reproducing the Figures can be found in this processed data dropbox folder also in this Figshare link.
The source data for each figure and supplementary table (in xlsx format, separate tabs) can be found here.