CRISPR-KO screen in HT29 cells for host factors for BFT toxicity

This repository contains code relevant to the publication A pro-carcinogenic bacterial toxin binds claudin-4 to cleave E-cadherin, by the authors Maxwell T. White, Kang Wang, Hailong Zhang, Ulrich Eckhard, Karthik Hullahalli, Jason Chen, Shaoguang Wu, Abby L. Geis, Jie Zhang, Jessica Queen, F. Xavier Gomis-Ruth, Matthew K. Waldor, Min Dong, and Cynthia L. Sears. READ ME: This work flow uses miniconda3 (Python version 3.12.8) with the package MAGeCK (https://sourceforge.net/projects/mageck/). The script CRISPR-count.zsh performs the analysis of the fastq files A-mw1.fastq, B-mw1.fastq, A1R1-mw1.fastq, B1R1-mw1.fastq, A1R2-mw1.fastq, and B1R2-mw1.fastq to determine sgRNA counts per population and compute gene-level enrichment scores in selected populations compared to the input populations. BFT treatment of Avana library A and selection of the top 10% of cells by surface E-cadherin staining yielded population A1R1 (R1 for the first round of selection), while performing the same selection on the expanded population A1R1 yielded population A1R2. The same is true for populations B1R1 and B1R2 deriving from Avana library B. The volcano plots in Fig. 1b are A1R1vsA (top left), A1R2vsA (top right), B1R1vsB (bottom left), and B1R2vsB (bottom right).