ArticlePlant physiology2004
Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis.
Article in Plant physiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling.PloS one · 2019Article
- Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing.Frontiers in genetics · 2019Review
- Review
- Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.BMC genomics · 2015Article
- Detecting and comparing non-coding RNAs in the high-throughput era.International journal of molecular sciences · 2013Review
- Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE library.TheScientificWorldJournal · 2013Review
- Deeply dissecting stemness: making sense to non-coding RNAs in stem cells.Stem cell reviews and reports · 2012Review
- New insights in the sugarcane transcriptome responding to drought stress as revealed by superSAGE.TheScientificWorldJournal · 2012Article
- Direct and rapid detection of RNAs on a novel RNA microchip.Chembiochem : a European journal of chemical biology · 2010Article
- Article
- Global expression profiling in epileptogenesis: does it add to the confusion?Brain pathology (Zurich, Switzerland) · 2010Review
- Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus.BMC genomics · 2009Article
- Translational genomics for bioenergy production: there's room for more than one model.The Plant cell · 2007Article
- RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection.Molecular genetics and genomics : MGG · 2007Article
- Genomic and population analyses of the mating type loci in Coccidioides species reveal evidence for sexual reproduction and gene acquisition.Eukaryotic cell · 2007Article
- Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice.Plant physiology · 2007Article
- Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.Genome research · 2007Article
- The TIGR Rice Genome Annotation Resource: improvements and new features.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
- Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes.Plant physiology · 2006Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Serial analysis of gene expression (SAGE) is a widely used technique for large-scale transcriptome analysis in mammalian systems. Recently, a modified version called LongSAGE (S. Saha, A.B. Sparks, C. Rago, V. Akmaev, C.J. Wang, B. Vogelstein, K.W. Kinzler [2002] Nat Biotechnol 20: 508-512) was reported by increasing tag length up to 21 bp. Although the procedures for these two methods are similar, a detailed protocol for LongSAGE library construction has not been reported yet, and several technical difficulties associated with concatemer cloning and purification have not been solved. In this study, we report a substantially improved LongSAGE method called Robust-LongSAGE, which has four major improvements when compared with the previously reported protocols. First, a small amount of mRNA (50 ng) was enough for a library construction. Second, enhancement of cDNA adapter and ditag formation was achieved through an extended ligation period (overnight). Third, only 20 ditag polymerase chain reactions were needed to obtain a complete library (up to 90% reduction compared with the original protocols). Fourth, concatemers were partially digested with NlaIII before cloning into vector (pZEro-1), greatly improving cloning efficiency. The significant contribution of Robust-LongSAGE is that it solved the major technical difficulties, such as low cloning efficiency and small insert sizes associated with existing SAGE and LongSAGE protocols. Using this protocol, one can generate two to three libraries, each containing over 4.5 million tags, within a month. We recently have constructed five libraries from rice (Oryza sativa), one from maize (Zea mays), and one from the rice blast fungus (Magnaporthe grisea).
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