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Scientific article
Open access
English

Efficient targeted transcript discovery via array-based normalization of RACE libraries

Published inNature methods, vol. 5, no. 7, p. 629-635
Publication date2008
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.

Keywords
  • Alternative Splicing
  • Chromosomes, Human, Pair 21/genetics
  • Chromosomes, Human, Pair 22/genetics
  • Cloning, Molecular
  • DNA, Complementary/ genetics
  • Exons
  • Gene Expression Profiling/ methods
  • Gene Library
  • Genome, Human
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Amplification Techniques/ methods
  • Oligonucleotide Array Sequence Analysis/methods
  • Protein Isoforms/genetics
  • RNA/ genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcription, Genetic
Citation (ISO format)
DJEBALI, Sarah et al. Efficient targeted transcript discovery via array-based normalization of RACE libraries. In: Nature methods, 2008, vol. 5, n° 7, p. 629–635. doi: 10.1038/nmeth.1216
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Article (Published version)
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ISSN of the journal1548-7091
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