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SMARTer single cell total RNA-sequencing

Karen Verboom, Celine Everaert (UGent) , Nathalie Bolduc, Kenneth Livak, Nurten Yigit (UGent) , Dries Rombaut, Jasper Anckaert (UGent) , Simon Lee, Morten Venø, Jørgen Kjems, et al.
(2019) NUCLEIC ACIDS RESEARCH. 47(16).
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Abstract
Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3' end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation and on two other cancer cell lines sorted in microplates. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.
Keywords
GENOME-WIDE, SEQ, REVEALS, GENE, TRANSCRIPTOME, EXPRESSION, LANDSCAPE

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Citation

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MLA
Verboom, Karen, et al. “SMARTer Single Cell Total RNA-Sequencing.” NUCLEIC ACIDS RESEARCH, vol. 47, no. 16, 2019, doi:10.1093/nar/gkz535.
APA
Verboom, K., Everaert, C., Bolduc, N., Livak, K., Yigit, N., Rombaut, D., … Vandesompele, J. (2019). SMARTer single cell total RNA-sequencing. NUCLEIC ACIDS RESEARCH, 47(16). https://doi.org/10.1093/nar/gkz535
Chicago author-date
Verboom, Karen, Celine Everaert, Nathalie Bolduc, Kenneth Livak, Nurten Yigit, Dries Rombaut, Jasper Anckaert, et al. 2019. “SMARTer Single Cell Total RNA-Sequencing.” NUCLEIC ACIDS RESEARCH 47 (16). https://doi.org/10.1093/nar/gkz535.
Chicago author-date (all authors)
Verboom, Karen, Celine Everaert, Nathalie Bolduc, Kenneth Livak, Nurten Yigit, Dries Rombaut, Jasper Anckaert, Simon Lee, Morten Venø, Jørgen Kjems, Franki Speleman, Pieter Mestdagh, and Jo Vandesompele. 2019. “SMARTer Single Cell Total RNA-Sequencing.” NUCLEIC ACIDS RESEARCH 47 (16). doi:10.1093/nar/gkz535.
Vancouver
1.
Verboom K, Everaert C, Bolduc N, Livak K, Yigit N, Rombaut D, et al. SMARTer single cell total RNA-sequencing. NUCLEIC ACIDS RESEARCH. 2019;47(16).
IEEE
[1]
K. Verboom et al., “SMARTer single cell total RNA-sequencing,” NUCLEIC ACIDS RESEARCH, vol. 47, no. 16, 2019.
@article{8617976,
  abstract     = {{Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3' end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation and on two other cancer cell lines sorted in microplates. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.}},
  articleno    = {{e93}},
  author       = {{Verboom, Karen and Everaert, Celine and Bolduc, Nathalie and Livak, Kenneth and Yigit, Nurten and Rombaut, Dries and Anckaert, Jasper and Lee, Simon and Venø, Morten and Kjems, Jørgen and Speleman, Franki and Mestdagh, Pieter and Vandesompele, Jo}},
  issn         = {{0305-1048}},
  journal      = {{NUCLEIC ACIDS RESEARCH}},
  keywords     = {{GENOME-WIDE,SEQ,REVEALS,GENE,TRANSCRIPTOME,EXPRESSION,LANDSCAPE}},
  language     = {{eng}},
  number       = {{16}},
  pages        = {{12}},
  title        = {{SMARTer single cell total RNA-sequencing}},
  url          = {{http://doi.org/10.1093/nar/gkz535}},
  volume       = {{47}},
  year         = {{2019}},
}
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