ArticleScientific reports2019
Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 42 citations in OpenAlex.
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- Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations.Scientific reports · 2025Article
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- Proof of Concept Study: Comparison of Semi-Automated RNA Isolation Methods from Archived Formalin-Fixed, Paraffin-Embedded Tissues with Clinical Routine RNA Isolation Methods.Methods and protocols · 2024Article
- Exosomal mRNA Cargo are biomarkers of tumor and immune cell populations in pediatric osteosarcoma.Translational oncology · 2024Article
- A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials.Nature communications · 2024Article
- Comparative transcriptomic analysis reveals differences in gene expression and regulatory pathways between nonacral and acral melanoma in Asian individuals.The Journal of dermatology · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq.Advanced genetics (Hoboken, N.J.) · 2023Review
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- Systematic comparative analysis of strand-specific RNA-seq library preparation methods for low input samples.Scientific reports · 2022Article
- Boosting the power of transcriptomics by developing an efficient gene expression profiling approach.Plant biotechnology journal · 2022Article
- Transcriptome and Metabolome Analysis Revealed the Freezing Resistance Mechanism in 60-Year-Old OverwinteringBiology · 2021Article
- Transcriptomic profiling of human dental pulp cells treated with tricalcium silicate-based cements by RNA sequencing.Clinical oral investigations · 2021Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for diagnostics and alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging in some situations, for instance in cases of low input amounts or degraded RNA samples. Several protocols have been proposed to overcome these challenges, and many are available as commercial kits. In this study, we systematically test three recent commercial technologies for RNA-seq library preparation (TruSeq, SMARTer and SMARTer Ultra-Low) on human biological reference materials, using standard (1 mg), low (100 ng and 10 ng) and ultra-low (<1 ng) input amounts, and for mRNA and total RNA, stranded and unstranded. The results are analyzed using read quality and alignment metrics, gene detection and differential gene expression metrics. Overall, we show that the TruSeq kit performs well with an input amount of 100 ng, while the SMARTer kit shows decreased performance for inputs of 100 and 10 ng, and the SMARTer Ultra-Low kit performs relatively well for input amounts <1 ng. All the results are discussed in detail, and we provide guidelines for biologists for the selection of an RNA-seq library preparation kit.
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