SMARTer single cell total RNA-sequencing
| Autor: | Jo Vandesompele, Celine Everaert, Jørgen Kjems, Simon Lee, Morten T. Venø, Dries Rombaut, Kenneth J. Livak, Pieter Mestdagh, Nurten Yigit, Nathalie Bolduc, Jasper Anckaert, Karen Verboom, Frank Speleman |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
EXPRESSION
Sequence analysis RNA-Seq Computational biology Biology 03 medical and health sciences 0302 clinical medicine Circular RNA Cell Line Tumor REVEALS Genetics Humans Genomic library RNA Messenger TRANSCRIPTOME Gene Gene Library 030304 developmental biology 0303 health sciences LANDSCAPE Sequence Analysis RNA GENOME-WIDE High-Throughput Nucleotide Sequencing RNA Biology and Life Sciences RNA Circular Microfluidic Analytical Techniques Ribosomal RNA GENE Benchmarking SEQ Single cell sequencing RNA Ribosomal Methods Online Single-Cell Analysis Poly A 030217 neurology & neurosurgery |
| Zdroj: | NUCLEIC ACIDS RESEARCH Verboom, K, Everaert, C, Bolduc, N, Livak, K J, Yigit, N, Rombaut, D, Anckaert, J, Lee, S, Venø, M T, Kjems, J, Speleman, F, Mestdagh, P & Vandesompele, J 2019, ' SMARTer single cell total RNA sequencing ', Nucleic Acids Research, vol. 47, no. 16, e93 . https://doi.org/10.1093/nar/gkz535 Nucleic Acids Research |
| ISSN: | 0305-1048 |
| DOI: | 10.1093/nar/gkz535 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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