10x 3’ scRNA-seq analysis on Jurkat cells post TCR acivation in CRISPR/Cas9 screening

By performing 10x 3’ scRNA-seq on Jurkat cells post TCR acivation in CRISPR/Cas9 screening, we want to investigate the compatibility of the A/G mixed capture sequence on multiple single cell RNA-seq platforms. By mimicking the adenylated endogenous mRNA, gRNA transcripts could be directly captured by poly(dT) primer during the reverse transcription, and serve as perturbation index in high identification rate. In this study, we provided a framework of direct ‘genotyping’ for single cell CRISPR screen, by incorporating a capture sequence into the gRNA scaffold. With that, genotype, transcriptome and phenotype can be analyzed simultaneously. We used an A/G mixed capture sequence to mimic the poly(A) tail of pol II transcripts and facilitate the direct annealing of gRNA with poly(dT) RT primer that is widely used in versatile scRNA-seq platforms.