To refine the identification of CAR-Ts, we created a modified mm10 reference genome, by adding the WPRE sequence as additional gene, and run the alignment and quantification steps with the CellRanger v7.2.0 software (10X Genomics) on it. To reduce the number of false negative errors due to possible biases in the WPRE expression and to strengthen its signal, we employed the Markov Affinity-based Graph Imputation of Cells (**MAGIC**) technique.</br>
To refine the identification of CAR-Ts, we created a modified mm10 reference genome, by adding the WPRE sequence as additional gene, and run the alignment and quantification steps with the CellRanger v7.2.0 software (10X Genomics) on it. To reduce the number of false negative errors due to possible biases in the WPRE expression and to strengthen its signal, we employed the Markov Affinity-based Graph Imputation of Cells (**MAGIC**) technique.</br>
More precisely, starting from the input matrices we run the imputation on the Cd8a, Cd4, Cd3e, Cd14, Mki67, Top2a, and WPRE genes. Then, based on the distribution of the resulting imputed expression values of the WPRE sequence, CAR-Ts were selected among those belonging to Cd8-expressing clusters and displaying either basal or imputed WPRE expression higher than 0.05.
More precisely, starting from the input matrices we run the imputation on the Cd8a, Cd4, Cd3e, Cd14, Mki67, Top2a, and WPRE genes. Then, based on the distribution of the resulting imputed expression values of the WPRE sequence, CAR-Ts were selected among those belonging to Cd8-expressing clusters and displaying either basal or imputed WPRE expression higher than 0.05.
- MAGIC_imputation.R: R script to perform imputation of WPRE counts to identify CART cells
- MAGIC_imputation_plot.R: R script to produce paper plots
