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Custom long non-coding RNA capture enhances detection sensitivity in different human sample types

Annelien Morlion (UGent) , Celine Everaert (UGent) , Justine Nuytens (UGent) , Eva Hulstaert (UGent) , Jo Vandesompele (UGent) and Pieter Mestdagh (UGent)
(2021) RNA BIOLOGY. 18(Supplement 1). p.215-222
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Abstract
Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.
Keywords
lncRNA, RNA sequencing, probes, lncRNome, RNA abundance, RNA expression, FFPE, biofluid, LANDSCAPE

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MLA
Morlion, Annelien, et al. “Custom Long Non-Coding RNA Capture Enhances Detection Sensitivity in Different Human Sample Types.” RNA BIOLOGY, vol. 18, no. Supplement 1, 2021, pp. 215–22, doi:10.1080/15476286.2021.1971438.
APA
Morlion, A., Everaert, C., Nuytens, J., Hulstaert, E., Vandesompele, J., & Mestdagh, P. (2021). Custom long non-coding RNA capture enhances detection sensitivity in different human sample types. RNA BIOLOGY, 18(Supplement 1), 215–222. https://doi.org/10.1080/15476286.2021.1971438
Chicago author-date
Morlion, Annelien, Celine Everaert, Justine Nuytens, Eva Hulstaert, Jo Vandesompele, and Pieter Mestdagh. 2021. “Custom Long Non-Coding RNA Capture Enhances Detection Sensitivity in Different Human Sample Types.” RNA BIOLOGY 18 (Supplement 1): 215–22. https://doi.org/10.1080/15476286.2021.1971438.
Chicago author-date (all authors)
Morlion, Annelien, Celine Everaert, Justine Nuytens, Eva Hulstaert, Jo Vandesompele, and Pieter Mestdagh. 2021. “Custom Long Non-Coding RNA Capture Enhances Detection Sensitivity in Different Human Sample Types.” RNA BIOLOGY 18 (Supplement 1): 215–222. doi:10.1080/15476286.2021.1971438.
Vancouver
1.
Morlion A, Everaert C, Nuytens J, Hulstaert E, Vandesompele J, Mestdagh P. Custom long non-coding RNA capture enhances detection sensitivity in different human sample types. RNA BIOLOGY. 2021;18(Supplement 1):215–22.
IEEE
[1]
A. Morlion, C. Everaert, J. Nuytens, E. Hulstaert, J. Vandesompele, and P. Mestdagh, “Custom long non-coding RNA capture enhances detection sensitivity in different human sample types,” RNA BIOLOGY, vol. 18, no. Supplement 1, pp. 215–222, 2021.
@article{8735834,
  abstract     = {{Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.}},
  author       = {{Morlion, Annelien and Everaert, Celine and Nuytens, Justine and Hulstaert, Eva and Vandesompele, Jo and Mestdagh, Pieter}},
  issn         = {{1547-6286}},
  journal      = {{RNA BIOLOGY}},
  keywords     = {{lncRNA,RNA sequencing,probes,lncRNome,RNA abundance,RNA expression,FFPE,biofluid,LANDSCAPE}},
  language     = {{eng}},
  number       = {{Supplement 1}},
  pages        = {{215--222}},
  title        = {{Custom long non-coding RNA capture enhances detection sensitivity in different human sample types}},
  url          = {{http://dx.doi.org/10.1080/15476286.2021.1971438}},
  volume       = {{18}},
  year         = {{2021}},
}

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