Reaping the high hanging fruits of gene expression
GenXPro's SuperSAGE is the most advanced derivate of the "Serial Analysis of Gene Expression" (SAGE)- technology.
In contrast to its predecessor techniques, SAGE and LongSAGE with tags of only 14-18 bp respectively, SuperSAGE analyses highly specific tags of 26 bp.
In combination with novel high-throughput sequencing technologies, this highly-specific 26 bp tag-based approach allows for ultra-deep analysis of any eukaryotic transcriptome. No other gene-expression profiling technique provides the accuracy and cost efficiency of SuperSAGE.
GenXPro's SuperSAGE technology defines
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what gene is transcribed,
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how many times the gene is transcribed,
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and into what transcript isoforms it is transcribed,
by analysing and counting a diagnostic "tag"-sequence specific for each individual mRNA
of any eukaryotic organism's cells, tissues or organs, independently of the knowledge
of the genome (-> non-model organisms).
This „open architecture“ approach has numerous advantages over most microarray-platforms, since any transcript, known or unknown, can be identified and exactly quantified (->"counted not measured").
Together, SuperSAGE combines the advantages of the open architecture system as e.g. SAGE™ with an increased specificity of the tag—gene annotation, making it ideal for the analysis of unknown genomes and the identification of new transcripts.
Unequivocal annotation of the corresponding gene
The 26 bp tag is highly specific and can exactly be annotated to the corresponding gene with an e-value of 3-e005 in the NCBI Blast db.
Many transcript isoforms from one gene, or members of a gene family can be discovered.
Natural antisense transcripts (NATs) of both the cis- and the trans-type can be detected.
Highly specific primer and probe design for downstream applications
Any unknown transcript represented as a 26 bp tag can be studied in more detail via downstream PCR techniques, like 3' and 5'RACE or chromosome walking. Generally, the Tm of a 26 bp product is in the range of 50-70°C, allowing for highly specific PCR priming conditions. Alternatively, the highly specific tag can be used as probe to identify colonies within a cloned gene- or cDNA-bank.
Superior to micorarrays
SuperSAGE overcomes the major drawbacks of most microarrays.
Reliable quantification
because ditag-amplification errors can be eliminated in sillico, SuperSAGE provides a reliable quantification of any transcipt including rare transcipts.
Analysis of rare transcripts
90-95% of all transcipt-species are expressed in only 1-5 copies per cell, among them important transciption factors and other key regulators of the cells fate. However, these rare transciptts are invisible or bearly quantifiable on microarrays. By analysing hundred-thousands of 26 bp tags, these rare transcipts can be reilable quantified with SuperSAGE.
Analysis of host-parasite interactions
The precise annotation allows to simultaneously decipher the interplay of the transcriptomes of two or more organisms as e.g. a host and a parasite in their natural environments (Matsumura et. al., 2003) or to study transcriptomes of xeno-graft model systems.
