GSE163089
Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells
Single-cell RNA sequencing in principle offers unique opportunities to improve the efficacy of contemporary T-cell based immunotherapy against cancer. The use of high-quality single-cell data will aid our incomplete understanding of molecular programs determining the differentiation and functional heterogeneity of cytotoxic T lymphocytes (CTLs)  allowing for optimal therapeutic design. So far  a major obstacle to high depth single-cell analysis of CTLs is the minute amount of RNA available  leading to low capturing efficacy. To overcome this  we tailor a droplet-based approach for high-throughput analysis (tDrop-seq) and a plate-based method for high-performance in-depth CTL analysis (tSCRB-seq). The latter gives  on average  a 15-fold higher number of captured transcripts per gene compared to droplet-based technologies. The improved dynamic range of gene detection gives tSCRB-seq an edge in resolution sensitive downstream applications such as graded high confidence gene expression measurements and cluster characterization. We demonstrate the power of tSCRB-seq by revealing the subpopulation-specific expression of co-inhibitory and co-stimulatory receptor targets of key importance for immunotherapy. Overall design: This study groups a total of 27 samples of single-cell RNA sequencing with two different protocols (Drop-seq and SCRB-seq) and their modifications.