ArticleNature communications2023
TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 30 citations in OpenAlex.
- Review
- NanoTS: a deep learning tool for accurate SNP calling in nanopore long-read transcriptome data.Nature methods · 2026Article
- Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for characterization of low-to-moderate abundance isoforms.NAR genomics and bioinformatics · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms.Nature communications · 2026Article
- Decoding Immune Regulation: From Genetic Variation to Mechanism Through Single-Cell Genomics.Immune network · 2026Review
- Hybrid untargeted short-read and targeted long-read RNA sequencing facilitates genotype-phenotype associations at single-cell resolution.Genome biology · 2026Article
- Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation.Science advances · 2026Article
- The splice of life: how alternative splicing shapes regulatory and phenotypic evolution.The EMBO journal · 2026Review
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- PRICE: direct and robust detection of microRNAs at single-nucleotide resolution.Nature communications · 2026Article
- Fibroblastic FLT3L supports lymph node dendritic cells in the interfollicular niche.Nature immunology · 2025Article
- Cell-type-resolvedbioRxiv : the preprint server for biology · 2025Article
- Transposable elements drive species-specific and tissue-specific transcriptomes in human development.Genome biology · 2025Article
- Evaluating the potential and limitations of nanopore adaptive sampling for targeted transcriptome sequencing.Genome biology · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Transcript Identification Using Arrayed Hydrogels with TrapFISH.Advanced materials technologies · 2025Article
- Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification.Bioinformatics (Oxford, England) · 2025Article
- Long-read genome and RNA sequencing resolve a pathogenic intronic germline LINE-1 insertion in APC.NPJ genomic medicine · 2025Article
- Review
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
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Registered trials
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.