ArticleBMC genomics2022
A comparison of mRNA sequencing (RNA-Seq) library preparation methods for transcriptome analysis.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Genomic and transcriptomic sequencing in prostate cancer.Current opinion in oncology · 2025Review
- RNA Sequencing Protocols for Short-Read Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transcriptomic analysis reveals TME-mediated macrophage IFIT1 upregulation and CX3CR1 suppression drive osteosarcoma progression.Frontiers in oncology · 2025Article
- Comparison of RNA-Sequencing Methods for Degraded RNA.International journal of molecular sciences · 2024Article
- Identification of KRAS mutation-associated gut microbiota in colorectal cancer and construction of predictive machine learning model.Microbiology spectrum · 2024Article
- HA2-FimA DNA Vaccine Treats Experimental Periodontitis.Oral health & preventive dentistry · 2024Article
- Maternal PM2.5 exposure is associated with preterm birth and gestational diabetes mellitus, and mitochondrial OXPHOS dysfunction in cord blood.Environmental science and pollution research international · 2024Article
- A reliable and quick method for screening alternative splicing variants for low-abundance genes.PloS one · 2024Article
- LncRNA HOTAIR down-expression inhibits the invasion and tumorigenicity of epithelial ovarian cancer cells by suppressing TGF-β1 and ZEB1.Discover oncology · 2023Article
- ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.Nucleic acids research · 2023Article
- Review
- Transcriptome Sequencing ofPlants (Basel, Switzerland) · 2023Article
- Mosaic results after preimplantation genetic testing for aneuploidy may be accompanied by changes in global gene expression.Frontiers in molecular biosciences · 2023Article
- The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing.Life (Basel, Switzerland) · 2022Review
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3 authors.
Funding
Abstract
backgroundmRNA sequencing is a powerful technique, which is used to investigate the transcriptome status of a gene of interest, such as its transcription level and splicing variants. Presently, several RNA sequencing (RNA-Seq) methods have been developed; however, the relative advantage of each method has remained unknown. Here we used three commercially available RNA-Seq library preparation kits; the traditional method (TruSeq), in addition to full-length double-stranded cDNA methods (SMARTer and TeloPrime) to investigate the advantages and disadvantages of these three approaches in transcriptome analysis.
resultsWe observed that the number of expressed genes detected from the TeloPrime sequencing method was fewer than that obtained using the TruSeq and SMARTer. We also observed that the expression patterns between TruSeq and SMARTer correlated strongly. Alternatively, SMARTer and TeloPrime methods underestimated the expression of relatively long transcripts. Moreover, genes having low expression levels were undetected stochastically regardless of any three methods used. Furthermore, although TeloPrime detected a significantly higher proportion at the transcription start site (TSS), its coverage of the gene body was not uniform. SMARTer is proposed to be yielded for nonspecific genomic DNA amplification. In contrast, the detected splicing event number was highest in the TruSeq. The percent spliced in index (PSI) of the three methods was highly correlated.
conclusionsTruSeq detected transcripts and splicing events better than the other methods and measured expression levels of genes, in addition to splicing events accurately. However, although detected transcripts and splicing events in TeloPrime were fewer, the coverage at TSS was highest. Additionally, SMARTer was better than TeloPrime with regards to the detected number of transcripts and splicing events among the understudied full-length double-stranded cDNA methods. In conclusion, for short-read sequencing, TruSeq has relative advantages for use in transcriptome analysis.
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