One of the widely used animal models in biomedical research is the Guinea Pig and except for an 81 spotted microarray for immune response genes there is no other comprehensive microarray for gene expression profiling in Guinea Pigs. The primary reason for this is that the sequencing for the guinea pig has not been adequately completed to enable robust microarray design and validation. We have sought to overcome this limitation by the novel extension of cross species hybridization.

Design of Mammalian 244,000 probe array of sequenced species: We first designed a mammalian 244,000 probe array using mRNA sequences taken from 14 mammalian species including mRNA sequences available for guinea pigs also.

Hybridization with pooled Guinea Pig RNA and genomic DNA: The mammalian 244k gene expression array was hybridized with pooled Guinea pig RNA labeled with Cy3 and genomic DNA labeled with Cy5 together. The best hybridized probes for each gene (identified by each gene symbol) were selected based on the total intensity in Cy3 and Cy5 with bias to gene expression (Cy3) intensity.

Design of 44,000 probe Guinea Pig array:  The goal was to design array for the guinea pig with cross hybridizing probes, adding probes for sequences available for the species in NCBI, sequences from customer proprietary database and multiple probes for Genes of interest.

A total of 20023 out of 62560 probes representing different genes were selected. Best probes for each EST were selected based on the total intensity in Cy3 and Cy5 with bias to gene expression (Cy3) intensity. A total of 9823 out of 92815 probes were selected using these criteria. All the 1132 probes were guinea pig were taken and an additional 12925 good probes, designed from 19975 newly added EST’s in NCBI were taken up for filling the 44K array.

The 44k Guinea Pig array has been validated with several rounds of experiments and this is the only comprehensive gene expression microarray for guinea pig available in the market right now. This work was done in collaboration with Prof. Anil. Tyagi’s laboratory at the University of Delhi, South campus, New Delhi, India.

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To place an order for Guinea Pig Microarray, download the order form and send it to us at contact@genotypic.co.in.