ArticleNature communications2024
CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.
Article in Nature communications, 2024. 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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20 citing papers in PubMed.
- Review
- Towards mRNA therapeutics 2.0.Nature reviews. Drug discovery · 2026Review
- Protocol for simultaneous profiling of transcription start sites and full-length transcripts from low-input samples using Smart-seq+5'.STAR protocols · 2026Article
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- Epigenetic characterization of pseudogenes across human tissues.Genome research · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- TEITbase: a database for transposable element (TE)-initiated transcripts in human cancers.Database : the journal of biological databases and curation · 2026Article
- Systematic evaluation of long- and short-read RNA-seq for human peripheral blood.NAR molecular medicine · 2026Article
- Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation.Nature communications · 2025Article
- Transposable elements drive species-specific and tissue-specific transcriptomes in human development.Genome biology · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads.Genome research · 2025Article
- GENCODE 2025: reference gene annotation for human and mouse.Nucleic acids research · 2025Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.bioRxiv : the preprint server for biology · 2024Article
- SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.bioRxiv : the preprint server for biology · 2024Article
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.Genome biology · 2024Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.Genome biology · 2023Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.bioRxiv : the preprint server for biology · 2023Article
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.bioRxiv : the preprint server for biology · 2023Article
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Abstract
Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we develop CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5' capped, full-length transcripts. In our study, we evaluate the performance of CapTrap-seq alongside other widely used RNA-seq library preparation protocols in human and mouse tissues, employing both ONT and PacBio sequencing technologies. To explore the quantitative capabilities of CapTrap-seq and its accuracy in reconstructing full-length RNA molecules, we implement a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation. Our benchmarks, incorporating the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) data, demonstrate that CapTrap-seq is a competitive, platform-agnostic RNA library preparation method for generating full-length transcript sequences.
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