2018
DOI: 10.1101/328328
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Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

Abstract: We describe Droplet Assisted RNA Targeting by single cell sequencing (DARTseq), a versatile technology that enables multiplexed amplicon sequencing and transcriptome profiling in single cells. We applied DART-seq to simultaneously characterize the non-A-tailed transcripts of a segmented dsRNA virus and the transcriptome of the infected cell. In addition, we used DART-seq to simultaneously determine the natively paired, variable region heavy and light chain amplicons and the transcriptome of B lymphocytes.

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Cited by 13 publications
(14 citation statements)
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“…Newer 3′-based methods that allow for higher throughput, and greater sample sizes at reasonable cost, have allowed the identification of rarer populations, such as ε-cells ( 84 ). Targeted sequencing approaches, such as droplet-assisted RNA targeting by single-cell sequencing (DART-Seq), significantly improve coverage by targeting the limited depth of scRNA-Seq to a subset of preselected transcripts of interest ( 85 ). Computational methods are being developed to take into account and correct for confounding factors, such as donor genetic variation, dropout, and technical noise, although avoiding confounders will always be preferable to correcting for them through bioinformatic means ( 86 , 87 ).…”
Section: Future Outlookmentioning
confidence: 99%
“…Newer 3′-based methods that allow for higher throughput, and greater sample sizes at reasonable cost, have allowed the identification of rarer populations, such as ε-cells ( 84 ). Targeted sequencing approaches, such as droplet-assisted RNA targeting by single-cell sequencing (DART-Seq), significantly improve coverage by targeting the limited depth of scRNA-Seq to a subset of preselected transcripts of interest ( 85 ). Computational methods are being developed to take into account and correct for confounding factors, such as donor genetic variation, dropout, and technical noise, although avoiding confounders will always be preferable to correcting for them through bioinformatic means ( 86 , 87 ).…”
Section: Future Outlookmentioning
confidence: 99%
“…By synthesizing target sequence-linked beads, targeted sequences could be captured directly without laborious PCR amplification of each targeted sequence (32). Alternatively, ligating target sequences to conventional beads could also be used (33). Another application involves coupling of methods targeting individual cells using barcoding (34).…”
Section: Discussionmentioning
confidence: 99%
“…For example, single-cell profiling of BCR repertoires and transcriptomes has recently revealed a high degree of bystander activation during influenza vaccination 36 . This combined immune repertoire and transcriptome profiling has also been employed to obtain unprecedented resolution of lymphocyte dynamics in the context of cancer 41,42 .…”
Section: Introductionmentioning
confidence: 99%