ArticleInternational journal of molecular sciences2024
Comparison of RNA-Sequencing Methods for Degraded RNA.
Article in International journal of molecular sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A bone fragment-based protocol for RNA analysis of osteocyte-associated transcripts in surgically obtained human bone specimens.MethodsX · 2026Article
- Integrating zero-inflation correction and transcriptional kinetics for single-cell transcriptomic analysis.PLoS computational biology · 2026Article
- BCG overexpressing Ag85B reprograms host immune response through coordinated transcriptional networks.Frontiers in immunology · 2026Article
- Article
- Stromal transcriptomics uncover LIF as a key effector in high tumor budding triple-negative breast cancer.Scientific reports · 2025Article
- Commentary: a review of technical considerations for planning an RNA-Sequencing experiment.BMC genomics · 2025Review
- An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2025Article
- Efficient profiling of total RNA in single cells with STORM-seq.bioRxiv : the preprint server for biology · 2025Article
- Computational Comparison of Differential Splicing Tools for Targeted RNA Long-Amplicon Sequencing (rLAS).International journal of molecular sciences · 2025Article
- Fibroblast IRF7-mediated chondrocyte apoptosis affects the progression of collapse in steroid-induced osteonecrosis of the femoral head.Journal of orthopaedic surgery and research · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
RNA sequencing (RNA-Seq) is a powerful technique and is increasingly being used in clinical research and drug development. Currently, several RNA-Seq methods have been developed. However, the relative advantage of each method for degraded RNA and low-input RNA, such as RNA samples collected in the field of clinical setting, has remained unknown. The Standard method of RNA-Seq captures mRNA by poly(A) capturing using Oligo dT beads, which is not suitable for degraded RNA. Here, we used three commercially available RNA-Seq library preparation kits (SMART-Seq, xGen Broad-range, and RamDA-Seq) using random primer instead of Oligo dT beads. To evaluate the performance of these methods, we compared the correlation, the number of detected expressing genes, and the expression levels with the Standard RNA-Seq method. Although the performance of RamDA-Seq was similar to that of Standard RNA-Seq, the performance for low-input RNA and degraded RNA has decreased. The performance of SMART-Seq was better than xGen and RamDA-Seq in low-input RNA and degraded RNA. Furthermore, the depletion of ribosomal RNA (rRNA) improved the performance of SMART-Seq and xGen due to increased expression levels. SMART-Seq with rRNA depletion has relative advantages for RNA-Seq using low-input and degraded RNA.
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