ArticleNature methods2008
Efficient targeted transcript discovery via array-based normalization of RACE libraries.
Article in Nature methods, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 44 citations in OpenAlex.
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- Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.Genome research · 2012Article
- Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.Genome research · 2012Article
- Dark Matter RNA: Existence, Function, and Controversy.Frontiers in genetics · 2012Article
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- Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii.BMC genomics · 2011Article
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- RNA captor: a tool for RNA characterization.PloS one · 2011Article
- Inference of isoforms from short sequence reads.Journal of computational biology : a journal of computational molecular cell biology · 2011Article
- Deciphering squamous cell carcinoma using multidimensional genomic approaches.Journal of skin cancer · 2011Article
- Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.PloS one · 2010Article
- RNA dust: where are the genes?DNA research : an international journal for rapid publication of reports on genes and genomes · 2010Review
- Detection of novel 3' untranslated region extensions with 3' expression microarrays.BMC genomics · 2010Article
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22 authors at 8 institutions in 5 countries.
Funding
Abstract
Rapid amplification of cDNA ends (RACE) is a widely used approach for transcript identification. Random clone selection from the RACE mixture, however, is an ineffective sampling strategy if the dynamic range of transcript abundances is large. To improve sampling efficiency of human transcripts, we hybridized the products of the RACE reaction onto tiling arrays and used the detected exons to delineate a series of reverse-transcriptase (RT)-PCRs, through which the original RACE transcript population was segregated into simpler transcript populations. We independently cloned the products and sequenced randomly selected clones. This approach, RACEarray, is superior to direct cloning and sequencing of RACE products because it specifically targets new transcripts and often results in overall normalization of transcript abundance. We show theoretically and experimentally that this strategy leads indeed to efficient sampling of new transcripts, and we investigated multiplexing the strategy by pooling RACE reactions from multiple interrogated loci before hybridization.
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