ArticleGenome research2016
Improved definition of the mouse transcriptome via targeted RNA sequencing.
Article in Genome research, 2016. 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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Who cites it
20 citing papers in PubMed.
- Evaluating the reliability of tools for mRNA annotation and IRES studies.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the potential and limitations of nanopore adaptive sampling for targeted transcriptome sequencing.Genome biology · 2025Article
- RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts.bioRxiv : the preprint server for biology · 2024Article
- IsoVis - a webserver for visualization and annotation of alternative RNA isoforms.Nucleic acids research · 2024Article
- Fear extinction is regulated by the activity of long noncoding RNAs at the synapse.Nature communications · 2023Article
- Characterization of Ly108-H1 Signaling Reveals Ly108-3 Expression and Additional Strain-Specific Differences in Lupus Prone Mice.International journal of molecular sciences · 2023Article
- ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3.Cell reports · 2022Article
- Best practices on the differential expression analysis of multi-species RNA-seq.Genome biology · 2021Review
- Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).Methods in molecular biology (Clifton, N.J.) · 2021Article
- Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples.RNA biology · 2020Article
- Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease.Nature communications · 2020Article
- Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis.Frontiers in cardiovascular medicine · 2019Review
- Emerging Roles of Long Non-coding RNAs in Chronic Neuropathic Pain.Frontiers in neuroscience · 2019Review
- Towards a complete map of the human long non-coding RNA transcriptome.Nature reviews. Genetics · 2018Review
- Target-enrichment sequencing for detailed characterization of small RNAs.Nature protocols · 2018Article
- High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.Nature genetics · 2017Article
- Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.Journal of the American Chemical Society · 2017Article
- Genome annotation for clinical genomic diagnostics: strengths and weaknesses.Genome medicine · 2017Review
- When Long Noncoding RNAs Meet Genome Editing in Pluripotent Stem Cells.Stem cells international · 2017Review
- Understanding the Role of lncRNAs in Nervous System Development.Advances in experimental medicine and biology · 2017Review
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.
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