ArticleGenome research2003
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers, 1 of them a synthesis that pooled it.
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Who cites it
81 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Retinome - defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium.BMC genomics · 2004Pooled it
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- Bcl11b controls odorant receptor class choice in mice.Communications biology · 2019Article
- Towards a complete map of the human long non-coding RNA transcriptome.Nature reviews. Genetics · 2018Review
- Premature Expression of FOXO1 in Developing Mouse Pituitary Results in Anterior Lobe Hypoplasia.Endocrinology · 2018Article
- Paradigm shifts in genomics through the FANTOM projects.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Article
- Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.Nature communications · 2015Article
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- Notch/Rbpjκ signaling regulates progenitor maintenance and differentiation of hypothalamic arcuate neurons.Development (Cambridge, England) · 2013Article
- Disentangling the relationship between sex-biased gene expression and X-linkage.Genome research · 2012Article
- The forkhead transcription factor, Foxd1, is necessary for pituitary luteinizing hormone expression in mice.PloS one · 2012Article
- Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).PloS one · 2012Article
- Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.PloS one · 2012Article
- A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp.Marine biotechnology (New York, N.Y.) · 2011Review
- Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.Bioinformatics (Oxford, England) · 2011Article
- The reality of pervasive transcription.PLoS biology · 2011Article
- Computational methods for transcriptome annotation and quantification using RNA-seq.Nature methods · 2011Review
21 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
47 authors.
Funding
Abstract
We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs were enriched in full-length by Cap-Trapper,and in most cases,aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC),which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project,which also include non-protein-coding RNAs,and the lower gene number estimation of genome annotations. Altogether,5'-end clusters identify regions that are potential promoters for 8637 known genes and 5'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.
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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.