ArticleBMC genomics2017
A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 2 of them syntheses that pooled it.
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Who cites it
90 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Development and validation of urinary exosomal microRNA biomarkers for the diagnosis of acute rejection in kidney transplant recipients.Frontiers in immunology · 2023Pooled it
- The Caribbean-Hispanic Alzheimer's disease brain transcriptome reveals ancestry-specific disease mechanisms.Neurobiology of disease · 2023Pooled it
- Transcriptome profiling of human hypothalamic agouti-related protein and proopiomelanocortin neurons regulating energy homeostasis.Nature communications · 2026Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- To the homeRNAmax: Developing an Improved Blood Self-Collection and Stabilization Platform for Remote Transcriptomic Studies.Analytical chemistry · 2026Article
- Prolonged Sample Storage Reshapes the mInternational journal of molecular sciences · 2026Article
- Methods to Identify and Validate Therapeutic Targets Against Cancer-Associated Fibroblasts in Head and Neck Squamous Cell Carcinoma.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis.Computational and structural biotechnology journal · 2026Review
- Comparison of automated and manual mRNA enrichment to automated rRNA depletion for whole-blood RNA-sequencing.Scientific reports · 2025Article
- Transcriptomes of thirteen healthy feline tissue types.BMC genomics · 2025Article
- To the homeRNAmax: Developing an Improved Blood Self-Collection and Stabilization Platform for Remote Transcriptomic Studies.bioRxiv : the preprint server for biology · 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
- Development of an End-to-End Total RNA Sequencing Quality Control Framework for Blood-Based Biomarker Discovery.The Journal of molecular diagnostics : JMD · 2025Article
- Characterizing Non-T2 Asthma: Key Pathways and Molecular Implications Indicative of Attenuated Th2 Response.Inflammation · 2025Article
- Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants.Communications medicine · 2025Article
- Transcriptomics and epigenomics datasets of primary brain cancers in formalin-fixed paraffin embedded format.Scientific data · 2025Article
- Exploring the influence of pre-analytical variables on gene expression measurements and relative expression orderings in cancer research.Scientific reports · 2025Article
- Making sense of expanding transcriptomic data: network-based approaches for studying reproduction in domestic and wild animal species.Frontiers in veterinary science · 2025Review
- A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues.Life science alliance · 2024Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA-sequencing (RNA-seq) has emerged as one of the most sensitive tool for gene expression analysis. Among the library preparation methods available, the standard poly(A) + enrichment provides a comprehensive, detailed, and accurate view of polyadenylated RNAs. However, on samples of suboptimal quality ribosomal RNA depletion and exon capture methods have recently been reported as better alternatives.
methodsWe compared for the first time three commercial Illumina library preparation kits (TruSeq Stranded mRNA, TruSeq Ribo-Zero rRNA Removal, and TruSeq RNA Access) as representatives of these three different approaches using well-established human reference RNA samples from the MAQC/SEQC consortium on a wide range of input amounts (from 100 ng down to 1 ng) and degradation levels (intact, degraded, and highly degraded).
resultsWe assessed the accuracy of the generated expression values by comparison to gold standard TaqMan qPCR measurements and gained unprecedented insight into the limits of applicability in terms of input quantity and sample quality of each protocol. We found that each protocol generates highly reproducible results (R
conclusionsWe found that the ribosomal RNA depletion protocol from Illumina works very well at amounts far below recommendation and over a good range of intact and degraded material. We also infer that the exome-capture protocol (RNA Access, Illumina) performs better than other methods on highly degraded and low amount samples.
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