Development of a novel equine whole transcript oligonucleotide GeneChip microarray and its use in gene expression profiling of normal articular-epiphyseal cartilage.
BACKGROUND
No large scale equine microarray is available commercially to allow genomic and transcriptional profiling of the majority of genes that would define the genetic basis of equine disease.


OBJECTIVE
To generate a whole transcript target labelled GeneChip to interrogate the equine transcriptome and validate chip performance using RNA samples derived from organs, articular cells and normal cartilage.


METHODS
Equine mRNA and selected equine gene sequences derived from perfect cross-hybridisation of equine RNA on human microarray GeneChips, were used to design a custom equine gene microarray. Sequence data were used as a template for generation of a glass-slide based 5'-3' multi-exon-encompassing gene chip. The microarray was characterised using RNA derived from organs including spleen, liver, brain and kidney, and RNA from cultured chondrocytes, cartilage, synovial tissue and stem cells, employing a whole transcript target labelling assay to sample mRNA across the 5'-3' spectrum.


RESULTS
The custom microarray simultaneously interrogated over 12,300 equine specific genes. Probing the chip with mixtures of total RNA derived from parenchymatous organs and articular tissues resulted in 61.7 and 62.8% present calls, respectively. This gene chip provided expression information on up to 90% of the key molecules in important signalling, metabolic and development pathways. Cartilage specific matrix genes were abundantly expressed in normal articular cartilage, but surprisingly high levels of collagen types I, III, V and XI, reflected expression from the epiphyseal layers of maturing articular epiphyseal cartilage.


CONCLUSIONS
An oligonucleotide microarray with over 12,300 probe sets was generated by uniquely combining a labelling strategy incorporating expressed sequence tags from the entire transcriptome and supplementing selected human sequences that cross-hybridised with the horse. Validation showed robust performance of the microarray.


CONCLUSIONS
This array may be a useful tool to elucidate the pathogenesis of equine diseases.
Gläser
K E
KE
Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA.
Sun
Q
Q
Wells
M T
MT
Nixon
A J
AJ
D000818:Animals; D002358:Cartilage, Articular / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000662:veterinary; D005786:Gene Expression Regulation; D006132:Growth Plate / Q000378:metabolism*; D006736:Horses / Q000235:genetics* / Q000378:metabolism*; D046228:Microarray Analysis / Q000662:veterinary*; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary*