Use of the Affymetrix Human GeneChip array and genomic DNA hybridisation probe selection to study ovine transcriptomes

Abstract

Affymetrix GeneChip microarrays are a powerful tool to study global gene expression profiles and have been used on many species. However, no sheep-specific Affymetrix GeneChip is currently available and the bovine array is fairly limited in its coverage and annotation. Previously, a probe-selection method based on hybridisation of genomic DNA (gDNA) was developed, which enables GeneChips to be used for species that they were not designed for. This approach can greatly increase the number of potential annotated genes that can be studied beyond that which is currently available, particularly for species that do not have comprehensively characterised genomes. In this study, we demonstrate that gDNA-based probe selection on the Affymetrix Human U133+2 GeneChip array can be used to study gene expression profiles in sheep tissues. More than 20 000 transcripts were detected in triplicate ovine skeletal muscle and liver samples, which is more than would be possible using the commercially available sheep-specific microarray. The majority of the top 15 differentially expressed genes for each tissue were known to either be expressed in a tissue-specific manner or relate to specific functions of that tissue. Gene ontology analysis of the differentially expressed genes revealed the expected differences in gene expression profiles between the two tissues. Besides demonstrating that the probe selection method can be used to study the ovine transcriptome, the benefits of this approach are that it can greatly increase the number of annotated and novel genes that can be studied beyond those currently possible using ovine- or bovine-specific microarrays. This same method also has the potential to allow the study of other species where species-specific microarrays are not available or whose genomes have not been comprehensively characterised.

Genome-wide mRNA-seq profiling reveals predominant down-regulation of lipid metabolic processes in adipose tissues of Small Tail Han than Dorset sheep

“…Global gene expression profiling has been for over a decade mainly using microarray analysis [8,9]. In recent years, however, deep sequencing of transcriptomes is increasingly being utilized with promises of being higher sensitivity in identification of differential expression as well as holding opportunities to discover novel transcripts ( [13,20e22,33]).…”

Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe Level Data

“…Brassica oleracea L. (case 1) and Thlaspi caerulescens (case 2) were hybridised onto the Arabidopsis thaliana ATH1-121501 GeneChip ® Arrays [3,4] whereas the two animals (case 4 and 5) were hybridised onto the Human U133 Plus 2.0 Genome Arrays [22,23]. In the third case, the Affymetrix Rice Genome Array was used to investigate transcriptomic profiling related to drought stress in Musa [7].…”

A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress

“…For each genotype, custom CDF files were obtained, with reference to their gDNA hybridisation signal strength [36] for a subsequent estimation of the transcript levels. RNA CEL files were normalised in GeneSpring [37] using the Robust Multi-array Average.…”