ArticleNucleic acids research2006
Robust analysis of 5'-transcript ends (5'-RATE): a novel technique for transcriptome analysis and genome annotation.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Messenger RNAs of Yeast Virus-Like Elements Contain Non-templated 5' Poly(A) Leaders, and Their Expression Is Independent of eIF4E and Pab1.Frontiers in microbiology · 2019Article
- A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana.Scientific reports · 2016Article
- Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi.G3 (Bethesda, Md.) · 2015Article
- Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.The Plant cell · 2014Article
- 5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea.BMC genomics · 2013Article
- Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae.Nucleic acids research · 2010Article
- Noncanonical transcript forms in yeast and their regulation during environmental stress.RNA (New York, N.Y.) · 2010Article
- Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing.Molecular ecology · 2010Article
- Expansion mechanisms and functional annotations of hypothetical genes in the rice genome.Plant physiology · 2009Article
- From transcription start site to cell biology.Genome biology · 2009Review
- Pyrosequence analysis of expressed sequence tags for Manduca sexta hemolymph proteins involved in immune responses.Insect biochemistry and molecular biology · 2008Article
- Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system.BMC microbiology · 2008Article
- Article
- ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs).BMC genomics · 2007Article
- Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice.Plant physiology · 2007Article
- Targeted high-throughput sequencing of tagged nucleic acid samples.Nucleic acids research · 2007Article
- Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods.BMC genomics · 2006Article
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Complicated cloning procedures and the high cost of sequencing have inhibited the wide application of serial analysis of gene expression and massively parallel signature sequencing for genome-wide transcriptome profiling of complex genomes. Here we describe a new method called robust analysis of 5'-transcript ends (5'-RATE) for rapid and cost-effective isolation of long 5' transcript ends (approximately 80 bp). It consists of three major steps including 5'-oligocapping of mRNA, NlaIII tag and ditag generation, and pyrosequencing of NlaIII tags. Complicated steps, such as purification and cloning of concatemers, colony picking and plasmid DNA purification, are eliminated and the conventional Sanger sequencing method is replaced with the newly developed pyrosequencing method. Sequence analysis of a maize 5'-RATE library revealed complex alternative transcription start sites and a 5' poly(A) tail in maize transcripts. Our results demonstrate that 5'-RATE is a simple, fast and cost-effective method for transcriptome analysis and genome annotation of complex genomes.
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