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cells, cell, pubmed, article, sequencing, google, scholar, sequences, fig, cas, chains, sequence, tcr, single, supplementary, nanopore, analysis, gene, data, node, reads, central, bcr, rageseq, lymph, chain, performed, mrna, assigned, jurkat, fulllength, tumor, ramos, receptor, paired, genes, capture, targeted, lymphocytes, number, expression, vdj, nature, antigenreceptor, heavy, assembly, singlecell, methods, light, cancer,

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         headline:High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
         description:High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as antigen receptors. To overcome this limitation, we combined targeted capture and long-read sequencing of T-cell-receptor (TCR) and B-cell-receptor (BCR) mRNA transcripts with short-read transcriptome profiling of barcoded single-cell libraries generated by droplet-based partitioning. We show that Repertoire and Gene Expression by Sequencing (RAGE-Seq) can generate accurate full-length antigen receptor sequences at nucleotide resolution, infer B-cell clonal evolution and identify alternatively spliced BCR transcripts. We apply RAGE-Seq to 7138 cells sampled from the primary tumor and draining lymph node of a breast cancer patient to track transcriptome profiles of expanded lymphocyte clones across tissues. Our results demonstrate that RAGE-Seq is a powerful method for tracking the clonal evolution from large numbers of lymphocytes applicable to the study of immunity, autoimmunity and cancer. Single cell RNA sequencing generates short reads from one end of a template, providing incomplete transcript coverage and limiting identification of diverse sequences such as antigen receptors. Here the authors combine long read nanopore sequencing with short read profiling of barcoded libraries to generate full-length antigen receptor sequences.
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      headline:High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
      description:High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as antigen receptors. To overcome this limitation, we combined targeted capture and long-read sequencing of T-cell-receptor (TCR) and B-cell-receptor (BCR) mRNA transcripts with short-read transcriptome profiling of barcoded single-cell libraries generated by droplet-based partitioning. We show that Repertoire and Gene Expression by Sequencing (RAGE-Seq) can generate accurate full-length antigen receptor sequences at nucleotide resolution, infer B-cell clonal evolution and identify alternatively spliced BCR transcripts. We apply RAGE-Seq to 7138 cells sampled from the primary tumor and draining lymph node of a breast cancer patient to track transcriptome profiles of expanded lymphocyte clones across tissues. Our results demonstrate that RAGE-Seq is a powerful method for tracking the clonal evolution from large numbers of lymphocytes applicable to the study of immunity, autoimmunity and cancer. Single cell RNA sequencing generates short reads from one end of a template, providing incomplete transcript coverage and limiting identification of diverse sequences such as antigen receptors. Here the authors combine long read nanopore sequencing with short read profiling of barcoded libraries to generate full-length antigen receptor sequences.
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            address:
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            address:
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      affiliation:
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            address:
               name:Garvan Institute of Medical Research, Sydney, Australia
               type:PostalAddress
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            address:
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      email:[email protected]
PostalAddress:
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Kirby Institute for Infection and Immunity, School of Medical Sciences, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
      name:Garvan Institute of Medical Research, Sydney, Australia
      name:St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia

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