CAR-T immuno-therapies have been transformative solutions to treat cancer patients. As most CAR-T therapies rely on the introduction of CAR into host cells using lentiviral vectors followed by re-introducing modified T-cell back into patients, the quality of CAR-T is extensively regulated. Safety and efficacy attributes such as transduction efficiency and transgene copy number needs to be accurately measured. Mission Bio has developed a solution from panel design to data analysis for single-cell targeted DNA sequencing to interrogate transgenes. Using the Tapestri platform we demonstrate that single-cell DNA sequencing identifies transduced versus non-transduced cells with exceptional accuracy and precision, and measures the single-cell level vector copy number for populations of thousands of cells with single nucleotide resolution while reducing sample processing time from weeks to days. In addition, utilizing our oligo conjugated antibody system, we demonstrate single-cell multi-omics characterization of protein expression and transgene information of products.