The invention of massive parallel sequencing technologies is revolutionizing expression  analysis  by allowing qualitative as well as quantitative transcriptome analysis (SAGE, CAGE) in an easy and cost-effective way.

Advantages of Transcriptome Analysis by Next Generation Sequencing technology

• Using illumina sequencing technology,  4-5 million sequencing reads in a single flow cell channel  - 1/8th of a full system run – provide unprecedented coverage, sensitivity and dynamic range
• Transcripts with a single copy per cell can be picked up reliably in parallel to abundant mRNAs
• Tag based, quantitative expression analysis (e.g. SAGE or CAGE) with sufficient depth to obtain statistically meaningful results is achieved without need for tedious, expensive and time-consuming concatemerization and clone library generation
• Transcript variant discovery is feasible in an efficient way
• No establishment and maintenance of clone librairies is required
• Extremely quick – even for complex transcriptomes, data  of high quality and depth can be generated within 2 weeks after the libraries are ready

Our Service Offering:

• Conventional cDNA library sequencing, optionally using paired-end technology
• Digital Gene Expression Analysis, “Deep SAGE”  (according to illumina expression profiling technology)
   measurement of transcript abundancies based on 21bp tags derived from transcript 3’ ends
• Deep CAGE (licensed from DNAForm)  
  Capture of full length transcripts, measurement of transcript abundancies  based on 20bp tags derived from transcript 5’ ends
  Simultaneous mapping of transcriptional start sites, promoter localization
• Small RNA discovery and analysis (starting with clients’ RNA preparation)
• Bioinformatics:  mapping to reference transcriptome or genome
  

1. Harbers and Carninci: Tag-based approaches for transcriptome research and genome annotation; Nat. Meth. 2005, Vol. 2/7, 495-502
2. De Hoon and Hayashizaki: Deep cap analysis of gene expression (CAGE)- genome-wide identification of promoters, quantification of their expression, and network interference; Biotechniques 2008, Vol.44/5, 627-632 
3. Carninci et al.: Genome-wide analysis of mammalian promoter architecture and evolution; Nat. Genetics 2006, Vol. 38/6, 626-635