AAV-Perturb-seq

These notebooks contain code reproducing the single-cell analyses from:

Santinha, A.J., Klingler, E., Kuhn, M., Farouni, R., Lagler, S., Kalamakis, G., Lischetti, U., Jabaudon, D., & Platt, RJ., "AAV-mediated single-nucleus CRISPR screening of DiGeorge syndrome in vivo", Nature, 2023

Download the R objects from GEO to use the notebooks: GSE236519.

Count tables for gRNA expression libraries are generated as shown in Hill et al 2018 (https://github.com/shendurelab/single-cell-ko-screens.git)

Scripts in this repo:

• gRNA_nucleus_association.Rmd contains code for gRNA QC, filtering, and integration with gene expression data

• pooled_screen_analysis.Rmd accepts scRNA-seq screen data containing multiple cell types and perturbations

  • Filter non-perturbed cells with LDA
  • Create pseudobulks of perturbed cells
  • Calculate differential expression with edgeR using pseudobulks as input
  • Plot cell type-specific UMAPs with perturbed cells

• zigosity_analysis.Rmd contains code to separate perturbed cells by zygosity states

• lgdel_data_analysis.Rmd contains code to analyze the LgDel dataset and compare individual perturbations to the full deletion

• plot_functions.R contains support functions for plots

• dif.exp_functions.R contains support functions for filtering, differential expression, and data visualization