ArticleBMC genomics2008
A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A circuit perspective on narcolepsy.Sleep · 2020Article
- Cancer transcriptome profiling at the juncture of clinical translation.Nature reviews. Genetics · 2018Review
- A transcriptome study on Macrobrachium nipponense hepatopancreas experimentally challenged with white spot syndrome virus (WSSV).PloS one · 2018Article
- Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing.Biological research · 2015Article
- Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.BMC genomics · 2015Article
- Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.BMC genomics · 2015Article
- Dspp mutations disrupt mineralization homeostasis during odontoblast differentiation.American journal of translational research · 2015Article
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- Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis.BMC genomics · 2011Article
- The integrative analysis of microRNA and mRNA expression in mouse uterus under delayed implantation and activation.PloS one · 2010Article
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- Deep sequencing of coding and non-coding RNA in the CNS.Brain research · 2010Review
- Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology.BMC genomics · 2010Article
- An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.PLoS computational biology · 2009Article
- Next-generation tag sequencing for cancer gene expression profiling.Genome research · 2009Article
- A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling.BMC bioinformatics · 2009Article
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9 authors.
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Abstract
background"Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Parallel Signature Sequencing) are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered.
resultsIn order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method.
conclusionWe found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method.
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