QuantSeq. 3' Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis.
Sci Rep
; 9(1): 18895, 2019 12 11.
Article
em En
| MEDLINE
| ID: mdl-31827207
ABSTRACT
RNA-Seq is increasingly used for the diagnosis of patients, targeting of therapies and for single cell transcriptomics. These applications require cost effective, fast and reliable ways of capturing and analyzing gene expression data. Here we compared Lexogen's QuantSeq which captures only the 3' end of RNA transcripts and Illumina's TruSeq, using both Tophat2 and Salmon for gene quantification. We also compared these results to microarray. This analysis was performed on peripheral blood mononuclear cells stimulated with Poly (IC), a viral mimic that induces innate antiviral responses. This provides a well-established model to determine if RNA-Seq and QuantSeq identify the same biological signatures. Gene expression levels in QuantSeq and RNA-Seq were strongly correlated (Spearman's rho ~0.8), Salmon and Tophat2 (Spearman's rho > 0.9). There was high consistency in protein coding genes, non-concordant genes had a high proportion of shorter, non-coding features. RNA-Seq identified more differentially expressed genes than QuantSeq, both methods outperformed microarray. The same key biological signals emerged in each of these approaches. We conclude that QuantSeq, coupled with a fast quantification method such as Salmon, should provide a viable alternative to traditional RNA-Seq in many applications and may be of particular value in the study of the 3'UTR region of mRNA.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Leucócitos Mononucleares
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Análise de Sequência de RNA
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Perfilação da Expressão Gênica
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Sequenciamento de Nucleotídeos em Larga Escala
Limite:
Humans
Idioma:
En
Revista:
Sci Rep
Ano de publicação:
2019
Tipo de documento:
Article
País de afiliação:
Austrália