title: Deep-RACE: Comprehensive Search for Novel ncRNAs Associated to a Specific Locus.
abstract: Deep-RACE (or RACEseq) is a recently described method (Olivarius et al. BioTechniques 46(2):130-132, 2009) that applies next-generation sequencing to the Rapid Amplification of cDNA End (RACE) protocol to define the 5' and 3' ends of RNA transcripts. Conventional mapping of 5' and 3' ends is achieved by manually cloning the PCR product of RACE followed by Sanger sequencing; this process can become costly and time-consuming when investigating multiple transcripts. High-throughput sequencing of the RACE products streamlines this process by eliminating the need to manually cut bands from an agarose gel and to clone each product individually. Importantly, in addition to these advantages, next-generation sequencing can detect low abundance fragments that would be difficult to extract from gel and clone for Sanger sequencing. For these reasons, Deep-RACE is an ideal protocol for the comprehensive study of noncoding transcripts from both intergenic regions of the genome and from within the loci of protein coding genes.
authors.affiliation: Sylvester Comprehensive Cancer Center, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA. cpastori@med.miami.edu.
authors.forename: Chiara
authors.initials: C
authors.lastname: Pastori
authors.affiliation: Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, 1501 NW 10th Ave., Miami, FL, 33136, USA.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Velmeshev
authors.affiliation: Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
authors.forename: Veronica Julia
authors.initials: VJ
authors.lastname: Peschansky
mesh_terms: D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics*; D015723:Gene Library; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing; D021141:Nucleic Acid Amplification Techniques; D062085:RNA, Long Noncoding / Q000235:genetics; D022661:RNA, Untranslated; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated
keywords: 5′ and 3′ Rapid amplification of cDNA ends; Deep-RACE; Long noncoding RNAs; Next-generation sequencing; Transcriptome