A focused microarray to study human mitochondrial and nuclear gene expression.
A focused microarray (huMITOchip) was developed to study alterations of human mitochondrial and nuclear gene expression in health and disease. The huMITOchip contains 4,774 probe sets identical to the Affymetrix U 133 plus 2.0 chip covering genes affecting mitochondrial, lipid, cytokine, apoptosis, and muscle function transcripts. Unlike other gene chips, the huMITOchip has 51 probe sets that interrogate 37 genes of the mitochondrial genome. The human mitochondrial gene chip was validated against the Affymetrix U133 plus 2.0 array using an in vitro system of CCL136 muscle cell line stimulated with or without interferon gamma (IFN-gamma). The 37 genes from the mtDNA demonstrated absolute gene expression levels ranging from 0.1 to 3,182. The comparison of the two gene chips yielded an excellent Pearson's correlation coefficient (r = 0.98). At least 17 probe sets were differentially expressed in response to IFN-gamma on both chips, with a high degree of concordance. This is the first report on the development of a focused oligonucleotide microarray containing genes of the mitochondrial genome.
Voss
Joachim G
JG
Neuromuscular Diseases Section, National Institute of Neurological Diseases and Stroke, NIH, Bethesda, MD, USA. vossj@u.washington.edu
Raju
Raghavan
R
Logun
Carolea
C
Danner
Robert L
RL
Munson
Peter J
PJ
Rangel
Zoila
Z
Dalakas
Marinos C
MC
D000704:Analysis of Variance; D017209:Apoptosis / Q000235:genetics; D018929:Cell Culture Techniques; D002467:Cell Nucleus / Q000235:genetics*; D054357:Chemokine CXCL10 / Q000235:genetics; D054371:Chemokine CXCL11 / Q000235:genetics; D054370:Chemokine CXCL9 / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics*; D006801:Humans; D007249:Inflammation / Q000235:genetics; D032342:Muscle Cells / Q000166:cytology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D025341:Principal Component Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D015854:Up-Regulation / Q000235:genetics
D054357:Chemokine CXCL10; D054371:Chemokine CXCL11; D054370:Chemokine CXCL9; D004272:DNA, Mitochondrial; D004273:DNA, Neoplasm