ArticleNucleic acids research2013
Exome RNA sequencing reveals rare and novel alternative transcripts.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- The utility of ultra-deep RNA sequencing in Mendelian disorder diagnostics.American journal of human genetics · 2025Article
- The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples.Nucleic acids research · 2024Article
- Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases.Molecular therapy. Nucleic acids · 2024Review
- F5-Atlanta: A novel mutation in F5 associated with enhanced East Texas splicing and FV-short production.Journal of thrombosis and haemostasis : JTH · 2021Article
- Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples.RNA biology · 2020Article
- ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms.Nature communications · 2020Article
- Genetic basis of functional variability in adhesion G protein-coupled receptors.Scientific reports · 2019Article
- Targeted RNA-seq successfully identifies normal and pathogenic splicing events in breast/ovarian cancer susceptibility and Lynch syndrome genes.International journal of cancer · 2019Article
- Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events.Molecular biology and evolution · 2017Article
- A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples.BMC genomics · 2017Article
- Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle.Scientific reports · 2017Article
- RNA sequencing unravels the genetics of refractory/relapsed T-cell acute lymphoblastic leukemia. Prognostic and therapeutic implications.Haematologica · 2016Article
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.Nucleic acids research · 2016Review
- Article
- The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.Genome research · 2015Article
- RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.Cold Spring Harbor perspectives in medicine · 2015Review
- Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Sequencing depth and coverage: key considerations in genomic analyses.Nature reviews. Genetics · 2014Review
- Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network.BioMed research international · 2014Article
- An Island-Based Approach for Differential Expression Analysis.2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics : ACM - BCB 2013 : Washington, D.C., U.S.A., September 22 - 25, 2013. ACM Conference on Bioinformatics, Computational Biology and Biomedical Informa... · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA sequencing has become an important method to perform hypothesis-free characterization of global gene expression. One of the limitations of RNA sequencing is that most sequence reads represent highly expressed transcripts, whereas low level transcripts are challenging to detect. To combine the benefits of traditional expression arrays with the advantages of RNA sequencing, we have used whole exome enrichment prior to sequencing of total RNA. We show that whole exome capture can be successfully applied to cDNA to study the transcriptional landscape in human tissues. By introducing the exome enrichment step, we are able to identify transcripts present at very low levels, which are below the level of detection in conventional RNA sequencing. Although the enrichment increases the ability to detect presence of transcripts, it also lowers the accuracy of quantification of expression levels. Our results yield a large number of novel exons and splice isoforms, suggesting that conventional RNA sequencing methods only detect a small fraction of the full transcript diversity. We propose that whole exome enrichment of RNA is a suitable strategy for genome-wide discovery of novel transcripts, alternative splice variants and fusion genes.
Indexed as
Identifiers
What OpenQuestion holds
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.