ArticleScientific reports2019
Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction.
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 60 papers.
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Who cites it
60 citing papers in PubMed.
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- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- Pervasive enhanced transcription in inflammatory breast cancer tumors and PBMCs impacts RNA splicing and intronic RNAs in plasma.Science advances · 2026Article
- The regulation, function and disease relevance of cytoplasmic tRNAs.Nature reviews. Molecular cell biology · 2026Review
- Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae.Journal of visualized experiments : JoVE · 2026Article
- Dissecting the small RNA code of inflammatory bowel disease.Molecular medicine (Cambridge, Mass.) · 2026Article
- Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.Nature protocols · 2025Review
- Optimized identification and characterization of small RNAs with PANDORA-seq.Nature protocols · 2025Review
- FTO depletion does not alter mbioRxiv : the preprint server for biology · 2025Article
- A bacterial PrimPol-reverse transcriptase hybrid protein has a proofreading exonuclease activity that can be transferred to other reverse transcriptases.bioRxiv : the preprint server for biology · 2025Article
- Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.Molecular cell · 2025Article
- All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies.Nature reviews. Molecular cell biology · 2025Review
- Improved precision, sensitivity, and adaptability of ordered two-template relay cDNA library preparation for RNA sequencing.RNA (New York, N.Y.) · 2025Article
- tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation iniScience · 2024Article
- Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing.bioRxiv : the preprint server for biology · 2024Article
- Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini.Molecular cell · 2024Article
- Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers.PLoS genetics · 2024Article
- Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation.The Journal of cell biology · 2024Article
- Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Thermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by rationally designing RNA-seq adapters that minimize adapter dimer formation. Additionally, we developed biochemical and computational methods for remediating 5'- and 3'-end biases, the latter based on a random forest regression model that provides insight into the contribution of different factors to these biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5'- and 3'-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.