ArticleBMC genomics2019
A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.
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Who cites it
61 citing papers in PubMed, 1 synthesis or guideline pooled it.
- PancrESS - a meta-analysis resource for understanding cell-type specific expression in the human pancreas.BMC genomics · 2024Pooled it
- Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments.Genome biology and evolution · 2026Article
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Transcriptomic Analysis in the Liver of Two Rabbit Lines Divergently Selected for Intramuscular Fat Content.Animal genetics · 2026Article
- PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.Bioinformatics advances · 2026Article
- Expression of antibody-drug conjugate targets in post-mortem samples of breast cancer metastases and normal tissue.Nature communications · 2025Article
- Widespread sex-biased gene expression reflects female-biased longevity in a species with environmental sex determination.bioRxiv : the preprint server for biology · 2025Article
- Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring.RNA biology · 2025Article
- Landscape transcriptomics as a tool for addressing global change effects across diverse species.Molecular ecology resources · 2025Review
- APALORD: An R-based tool for differential alternative polyadenylation analysis of long-read RNA-seq data.bioRxiv : the preprint server for biology · 2025Article
- Optimizing Cost-Effective gene expression phenotyping approaches in cattle using 3' mRNA sequencing.BMC genomics · 2025Article
- Genome-wide transcriptome analysis reveals differentially expressed genes and key signalling pathways associated with cryptorchidism in pigs.Scientific reports · 2025Article
- Detecting gene expression in Caenorhabditis elegans.Genetics · 2025Review
- Strong correlation of gene counts and differentially expressed genes between a 3' RNA-Seq and an RNA hybridization platform in transcriptome analyses from canine archival tissues.Frontiers in veterinary science · 2025Article
- Genet identity and season drive gene expression in outplanted Acropora palmata at different reef sites.Scientific reports · 2024Article
- Whole-genome sequence ofMicrobiology resource announcements · 2024Article
- A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics.Briefings in bioinformatics · 2024Article
- Translatome profiling reveals Itih4 as a novel smooth muscle cell-specific gene in atherosclerosis.Cardiovascular research · 2024Article
- The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L.BMC plant biology · 2024Article
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
background3' RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and the 3' method is needed to determine their relative merits. To this end, we used two commercially available library preparation kits, the KAPA Stranded mRNA-Seq kit (traditional method) and the Lexogen QuantSeq 3' mRNA-Seq kit (3' method), to prepare libraries from mouse liver RNA. We then sequenced and analyzed the libraries to determine the advantages and disadvantages of these two approaches.
resultsWe found that the traditional whole transcript method and the 3' RNA-Seq method had similar levels of reproducibility. As expected, the whole transcript method assigned more reads to longer transcripts, while the 3' method assigned roughly equal numbers of reads to transcripts regardless of their lengths. We found that the 3' RNA-Seq method detected more short transcripts than the whole transcript method. With regard to differential expression analysis, we found that the whole transcript method detected more differentially expressed genes, regardless of the level of sequencing depth.
conclusionsThe 3' RNA-Seq method was better able to detect short transcripts, while the whole transcript RNA-Seq was able to detect more differentially expressed genes. Thus, both approaches have relative advantages and should be selected based on the goals of the experiment.
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