GenXPro - High-Throughput, Genome-Wide Gene Expression Activity Measurements

GenXPro is a service provider specialised in high-throughput, genome-wide gene expression activity measurements. GenXPro’s portfolio covers all transcription-based services for pharmacy, toxicology and individualised medicine, including the detection of new drug targets, development of biomarkers, analysis of drug responses and assessment of drug action and risk.

SuperSAGE and SuperTAG digital gene expression (DGE) profiling

GenXPro's SuperTAG digital gene expression platform (ST-DGE) is an adaptation of SuperSAGE, the most advanced derivative of the ‘Serial Analysis of Gene Expression’ (SAGE) technology, to high-throughput sequencing techniques like SOLEXA™ and SOLID™.

In contrast to its predecessors and other DGE platforms with tags of only 18-21bp, SuperSAGE and ST-DGE analyses several magnitudes more specific tags of 26bp. No other gene expression profiling technique provides the accuracy and cost efficiency of SuperSAGE.

Advantages of SuperTAG digital gene expression (ST-DGE)

GenXPro's digital gene expression technology defines what gene is transcribed and how many times it is transcribed by counting millions of diagnostic 26bp tag sequences, which are specific for each individual mRNA. The advantages are:

• Open-architecture technology: any transcript will be detected and reliably quantified including new transcripts, antisense transcripts and low-abundance transcripts
• No technical detection limit; depending on the required level of analysis, transcription profiles comprise three to 20 million transcripts per sample
• The dynamic range comprises six orders of magnitude, several orders of magnitude more sensitive than gene expression arrays and quantitative Real-Time (qRT)-PCR
• No ambiguous signals, no cross-hybridization
• Measures gene activity simultaneously in two or more organisms
• Works with minute amounts of starting material
• Produces digital data
• Results are comparable between experiments and laboratories
• Comprehensive bioinformatic analysis and graphical display of results

Accuracy and analysis of new transcripts

The 26bp tag can 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 distinguished and natural antisense transcripts (NATs) can be analysed.

Any unknown transcript will be represented as a 26bp tag and can be studied in more detail via downstream PCR techniques, like 3'RACE and 5'RACE or chromosome walking, since the 26bp allows for highly specific PCR priming conditions.

Reliable quantification and rare transcripts

Because amplification errors can be eliminated in silico, SuperTAG-DGE provides a reliable quantification of any transcript. 90%-95% of all transcript-species are expressed in only one to five copies per cell, among them important transcription factors and other key regulators of the cell’s fate. However, these rare transcripts are invisible or barely quantifiable on microarrays. Our digital gene expression platforms can accurately quantify these transcripts.

Analysis of host-parasite interactions

Precise annotation allows for the simultaneous deciphering of the interplay of the transcriptomes of two or more organisms as, for example, a host and a parasite in their natural environments (Matsumura et. al., 2003), or to study transcriptomes of xeno-graft model systems.

GenXPro’s analysis of normalised cDNA

GenXPro has developed highly efficient protocols for the preparation and analysis of normalised cDNA so that abundant transcripts are efficiently reduced. Sequencing of the normalised cDNA will reflect up to 99% of all transcripts present in the cDNA population.

By combining SuperTAG-DGE with the sequence information of normalised cDNA, any non-model organism can be analysed in short time for very low costs.

Quantitative real-time-PCR

GenXPro's qRT-PCR service includes:

• Design and evaluation of qRT-PCR (TaqMan-based) assays
• High-fidelity transcription profiling of single to multiple transcripts in large numbers of samples
• Detection of SNPs and copy-number variations in genomic DNA
• Rigorous quality control
• Documentation and discussion of results with customers