Journal: The Journal of Biological Chemistry

Article Title: Laccaic Acid A Is a Direct, DNA-competitive Inhibitor of DNA Methyltransferase 1 *

doi: 10.1074/jbc.M113.480517

Figure Lengend Snippet: qPCR validation of LCA microarray analysis and changes in gene expression caused by treatment with control compound, anthraquinone-2-carboxylic acid

Article Snippet: Microarray Analysis Total RNA was isolated from 2 × 10 5 cells and used for microarray analysis (University of Iowa DNA Core Facility) in hybridization to Human Gene ST1.0 Array GeneChips (Affymetrix).

Techniques: Biomarker Discovery, Microarray, Gene Expression, Control

Journal: The Journal of Biological Chemistry

Article Title: Synthesis of Mitochondrial DNA Precursors during Myogenesis, an Analysis in Purified C2C12 Myotubes *

doi: 10.1074/jbc.M112.441147

Figure Lengend Snippet: Microarray analysis of genes regulating the dNTP pools in muscle cells. Samples were as follows: myoblasts ( Mb ), proliferating C2C12 myoblasts at 50% confluence; Myt , myotubes purified at 8 days of differentiation; EDL , extensor digitorum longus; and soleus ( SOL ), skeletal muscles dissected from adult CD1 mice. To measure expression levels, Cy3-labeled target from myoblasts, extensor digitorum longus and soleus preparations were hybridized in triplicate experiments on whole mouse genome oligonucleotide microarrays (4 × 44,000, Agilent Technologies). Normalized values were converted to log2 (scale on the left ), and heat maps were constructed with MultiExperiment Viewer to visualize gene expression levels. All genes involved in dNTP metabolism were annotated on the basis of their cytosolic or mitochondrial localization ( supplemental Table 1 ). To evaluate the significance of the expression changes, pairwise Significance Analysis of Microarrays two class analyses were carried out between myoblasts and each of the other samples. A , genes differentially expressed in at least one test using a false discovery rate of 1%. B , genes that showed no significant changes in muscle fibers compared with myoblasts. C , genes from A , sorted according to fold-change values to underline the predominant down-regulation observed in comparisons between cycling and differentiated muscle cells. A double asterisk marks genes with the most significant changes (false discovery rate, 0% in at least two tests). The inset shows the few genes with positive fold-changes.

Article Snippet: Incubation proceeded for 17 h at 65 °C at 10 rpm in a microarray hybridization oven (Agilent Technologies).

Techniques: Microarray, Purification, Expressing, Labeling, Construct