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High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

Mandeep Singh, Ghamdan Al-Eryani, View ORCID ProfileShaun Carswell, View ORCID ProfileJames M. Ferguson, James Blackburn, View ORCID ProfileKirston Barton, View ORCID ProfileDaniel Roden, View ORCID ProfileFabio Luciani, View ORCID ProfileTri Phan, View ORCID ProfileSimon Junankar, View ORCID ProfileKatherine Jackson, View ORCID ProfileChristopher C. Goodnow, View ORCID ProfileMartin A. Smith, View ORCID ProfileAlexander Swarbrick
doi: https://doi.org/10.1101/424945
Mandeep Singh
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Ghamdan Al-Eryani
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Shaun Carswell
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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  • ORCID record for Shaun Carswell
James M. Ferguson
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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James Blackburn
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Kirston Barton
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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  • ORCID record for Kirston Barton
Daniel Roden
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Fabio Luciani
2St Vincent’s Clinical School, UNSW Sydney, Australia
4Kirby Institute for Infection and Immunity, UNSW Sydney, Australia
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Tri Phan
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Simon Junankar
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Katherine Jackson
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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  • ORCID record for Katherine Jackson
Christopher C. Goodnow
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Martin A. Smith
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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Alexander Swarbrick
1Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
2St Vincent’s Clinical School, UNSW Sydney, Australia
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  • ORCID record for Alexander Swarbrick
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 24, 2018.
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High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
Mandeep Singh, Ghamdan Al-Eryani, Shaun Carswell, James M. Ferguson, James Blackburn, Kirston Barton, Daniel Roden, Fabio Luciani, Tri Phan, Simon Junankar, Katherine Jackson, Christopher C. Goodnow, Martin A. Smith, Alexander Swarbrick
bioRxiv 424945; doi: https://doi.org/10.1101/424945
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High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
Mandeep Singh, Ghamdan Al-Eryani, Shaun Carswell, James M. Ferguson, James Blackburn, Kirston Barton, Daniel Roden, Fabio Luciani, Tri Phan, Simon Junankar, Katherine Jackson, Christopher C. Goodnow, Martin A. Smith, Alexander Swarbrick
bioRxiv 424945; doi: https://doi.org/10.1101/424945

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