Detection of transcriptional difference of porcine imprinted genes using different microarray platforms.
BACKGROUND
Presently, multiple options exist for conducting gene expression profiling studies in swine. In order to determine the performance of some of the existing microarrays, Affymetrix Porcine, Affymetrix Human U133+2.0, and the U.S. Pig Genome Coordination Program spotted glass oligonucleotide microarrays were compared for their reproducibility, coverage, platform independent and dependent sensitivity using fibroblast cell lines derived from control and parthenogenic porcine embryos.


RESULTS
Array group correlations between technical replicates demonstrated comparable reproducibility in both Affymetrix arrays. Glass oligonucleotide arrays showed greater variability and, in addition, approximately 10% of probes had to be discarded due to slide printing defects. Probe level analysis of Affymetrix Human arrays revealed significant variability within probe sets due to the effects of cross-species hybridization. Affymetrix Porcine arrays identified the greatest number of differentially expressed genes amongst probes common to all arrays, a measure of platform sensitivity. Affymetrix Porcine arrays also identified the greatest number of differentially expressed known imprinted genes using all probes on each array, an ad hoc measure of realistic performance for this particular experiment.


CONCLUSIONS
We conclude that of the platforms currently available and tested, the Affymetrix Porcine array is the most sensitive and reproducible microarray for swine genomic studies.
Tsai
Shengdar
S
Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. shengdar_tsai@ncsu.edu <shengdar_tsai@ncsu.edu>
Mir
Bashir
B
Martin
Amy C
AC
Estrada
Jose L
JL
Bischoff
Steve R
SR
Hsieh
Wen-ping
WP
Cassady
Joseph P
JP
Freking
Bradley A
BA
Nonneman
Dan J
DJ
Rohrer
Gary A
GA
Piedrahita
Jorge A
JA
D000818:Animals; D020869:Gene Expression Profiling; D018392:Genomic Imprinting; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D013552:Swine / Q000235:genetics*; D014158:Transcription, Genetic