CAGE - Address the complexity of transcriptomes
The comprehensive characterization of the transcriptome comprising tens-of-thousands of genes regulated at various levels and differentially expressed on the cellular level is a challenging task, which has to be addressed by new approaches to uncover the entire complexity of individual transcriptomes. The first level of transcriptome regulation controls the expression of individual genes,
where the amounts of a given transcript can be correlated with the promoter activity of the associated gene.
RIKEN and DNAFORM jointly developed CAGE (Cap-Analysis-Gene-Expression) as a novel approach for expression profiling and promoter identification, which can the starting point for transcriptional network analysis and transcriptome characterization.
With the availability of next-generation sequencing methods, DNAFORM now offers DeepCAGE services. DeepCAGE libraries are prepared for direct analysis by an Illumina/Solexa Sequencer. One sequencing run using one channel on an Illumina/Solexa Sequencer can yield in over 4,000,000 reads per sample. DeepCAGE, the combination of next-generation sequencing with next generation expression profiling provides unsurpassed solutions for expression profiling and genome annotation.
CAGE - What can it do for you?
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Bring clarity into the heterogeneity and complexity of transcriptomes by changing the view from
expression profiling to the "Cause of Transcription".
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Link of expression values to promoter sites for a better understanding on how signaling pathways
influence transcription.
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Shifts the focus transcript analysis from 3'-end related information to 5'-ends of mRNA for the
identification of Transcriptional Start Sites (TSS).
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Data are unbiased to known transcripts and sequence information.
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Provides experimental validation for transcriptional start sites as computational methods cannot
predict end-points of transcripts.
CAGE - How does it work?
CAGE is based on our full-length cDNA library technology, where an adaptor is ligated to the 5'-end of full-length cDNAs, which introduces a recognition site for a Class IIs restriction endonuclease adjacent to the 5'-end of the cDNA. The Class IIs restriction endonuclease, here MmeI, allows for the cloning of short tags as derived from the 5'-end of transcripts into concatemers for high-throughput sequencing. CAGE tags are further characterized by mapping to genomic sequences, which enables the identification of transcriptional start sites. As such CAGE can contribute to projects in Gene Discovery, Gene Expression, and Promoter Identification.
CAGE - More than just expression profiling!
After the genome sequencing projects have provided us with the genetic blueprints for many organisms, new questions have to be answered on how to correlate the observed genotypes with related phenotypes, and how to understand the regulation of genetic information in time and space. The dynamics of living systems and the functional behavior of cells in multicellular organisms has thus become the subject of the emerging field of system biology. Integration of experimental approaches and computer aided theories on a system level will be the fundamental principle to drive systems biology in order to understand the principles behind complex regulatory networks, which will be an ambitious goal requiring new approaches in life sciences.
Here, CAGE will be the experimental approach at need to link gene expression and control regions in the genome. DNAFORM is ready to move forward into the upcoming area of systems biology.
For ordering and additional information, please contact us under contact@dnaform.jp
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