Splice Arrays

Jivan Biologics empowers scientists with new insight by providing a full catalogue of splice variant products and services for all stages of the drug development pipeline from target discovery, target validation and functional genomics to predictive toxicology, personalized medicine and the search for clinical markers in blood.

Available as a service since 2001 and as catalogue products since 2003, Jivan’s flagship SpliceExpress™ arrays are the first commercial microarrays for alternative splicing. Jivan also leads with software for alternative splicing analysis and PCR primer sets for splice isoform detection.

SpliceExpress™ arrays empower scientists to diagnose, profile and treat disease with greater precision.

Splice Array Design

Jivan’s splice array design begins with a database of splice isoforms compiled from the human genome, RefSeq and EST databases. Using genomic alignments, Jivan annotates exon boundaries and identifies distinct spliced products with sequence evidence as well as expected splice products based on predictive algorithms.

Then Jivan selects oligonucleotide probes specific to each splice site (exon-exon junction or exon-intron junction) of each gene product. Junction probes are capable of directly detecting any splicing event–including alternative exons, retained introns, alternative acceptor or donor sites leading to trimmed and extended exons–covering the whole spliceome.

Oligonucleotide probes range in length from 34 to 42 bases (T. Clark, C. Sugnet, M. Ares Jr., Science, 296, 907 (2002)) to achieve an isothermal target melting temperature (Tm) of approximately 67° array-wide. Further optimization balances the melting temperature of the probe on each side of the splice site for exon-exon and exon-intron junctions for cleaner differentiation between alternative splice sites.

Each SpliceExpress™ splice array contains junction probes for a collection of genes carefully selected for comprehensiveness and relevance based on publications, automated analysis and manual curation.

Sample Preparation and Hybridization Protocols

SpliceExpress™ microarrays for alternative splicing support a variety of standard protocols, reagant kits and equipment. Total RNA is the most common starting point for experiments with SpliceExpress™. For full service customers, we usually request 5µg of total RNA per sample per array. This is used for RNA purification and quality testing as well as for hybridization. The actual hybridization can be done with less than 1µg of RNA.

Several commercially available amplification and labeling kits work well. Kits that amplify RNA without 3′ bias are preferable because splicing may occur near the 5′ end of the gene. Jivan probes are optimized for use with standard hybridization protocols. We can make more detailed recommendations when an order is placed.

Scanners from Axon and Agilent can read the arrays and extract features.

For data analysis, Jivan’s splice arrays are compatible with standard software packages such as SpotFire, GeneSpring, Partek and Resolver. Full service customers can also benefit from Jivan’s proprietary data analysis methods, including deconvolution of exon-exon junction and exon-intron junction signals to identify splice products that span multiple probes.

For validation by rt-PCR, Jivan has a database of PCR primer designs capable of detecting the splice variants for each SpliceExpress™ product.

For specific protocol questions, please email us.

Jivan also offers full service for SpliceExpress™ splice arrays. Simply send us your samples, and we will do the experiments for you.