TY - JOUR T1 - High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes JF - bioRxiv DO - 10.1101/424945 SP - 424945 AU - Mandeep Singh AU - Ghamdan Al-Eryani AU - Shaun Carswell AU - James M. Ferguson AU - James Blackburn AU - Kirston Barton AU - Daniel Roden AU - Fabio Luciani AU - Tri Phan AU - Simon Junankar AU - Katherine Jackson AU - Christopher C. Goodnow AU - Martin A. Smith AU - Alexander Swarbrick Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/09/24/424945.abstract N2 - High-throughput single-cell RNA-Sequencing is a powerful technique for gene expression profiling of complex and heterogeneous cellular populations such as the immune system. However, these methods only provide short-read sequence from one end of a cDNA template, making them poorly suited to the investigation of gene-regulatory events such as mRNA splicing, adaptive immune responses or somatic genome evolution. To address this challenge, we have developed a method that combines targeted long-read sequencing with short-read based transcriptome profiling of barcoded single cell libraries generated by droplet-based partitioning. We use Repertoire And Gene Expression sequencing (RAGE-seq) to accurately characterize full-length T cell (TCR) and B cell (BCR) receptor sequences and transcriptional profiles of more than 7,138 lymphocytes sampled from the primary tumour and draining lymph node of a breast cancer patient. With this method we show that somatic mutation, alternate splicing and clonal evolution of T and B lymphocytes can be tracked across these tissue compartments. Our results demonstrate that RAGE-Seq is an accessible and cost-effective method for high-throughput deep single cell profiling, applicable to a wide range of biological challenges. ER -