Digital Gene Expression Profiling by SuperSAGE and MACE
SuperSAGE, an advanced version of Serial Analysis of gene Expressiom (SAGE) with longer cDNA tags, provides an ultra-deep analysis of any transcriptome by sequencing millions of transcript-specific fragments, each representing one mRNA molecule. MACE (Massive Analysis of cDNA Ends) is our latest adaptation of the tag-based approach, using even longer tags of up to 500 bases of the 3’-ends of cDNAs.
Resolution: Because each transcript is represented by only one tag, ST-DGE and MACE capture even low-level transcripts such as for receptors, transcription factors or naturally occurring antisense transcripts. These low-level transcripts are invisible on microarrays. Since up to 80% of a cell’s transcript species are expressed at low levels (1-20) copies per Million their analysis is crucial to understand the cells function. Our tag-based analyses display these low level transcripts for only 1/2 of the costs of RNA-Seq.
Quantification: All second- generation sequencing-based data are prone to PCR-bias, because different DNA fragments are amplified with different amplification efficiency. GenXPro has developed a method to eliminate such bias by its “PCR-Copy-Elimination” technique.
Scheme: cDNA, bound via a biotinylated 3'end to a streptavidin matrix is fragmented. To the bound fragments, a sequencing primer is ligated and the fragments are sequenced starting from the fragmentation site. The sequences are quantified and can be assembled. As 3' ends contain many SNPS and indels, this information can be used for example for marker deveolpment. Please click here for a more detailed presentation for MACE and for SuperSAGE
