Figure 5

Correspondence between Q-PCR and GeneChip data. Sixty male C57BL/6 mice were divided into 20 groups of 3 mice each. 2,3,7,8-tetrachlorodibenzodioxin (TCDD) was administered once orally at doses of 0, 1, 3, 10 and 30μg/kg, and the liver was sampled 2, 4, 8 and 24 h after administration. The liver transcriptome was measured by the Affymetrix Mouse430-2 GeneChip. For Q-PCR, nineteen primary pairs were prepared and the Ct values of the same 60 liver samples were measured (19 genes and 5 spikes in duplicate, using a 96-well plate for 2 samples, total 30 plates). The Percellome data were plotted on to 3-dimensional graphs for average, +1sd, and – 1sd surfaces as shown in (a). The scale of expression (vertical axis) is the copy number per cell. The 0 h data (*) are copied from the 2 h/dose 0 point for better visualization of the changes after 2 h. The surfaces are demonstrated as a grid plot (b) where the grid points indicate one treatment group (n = 3), and a smoothened spline surface plot (c) for easier 3D recognition ((b), (c): Gys2 (glycogen synthase 2, 1424815_ at) showing a typical circadian pattern. (d) the smoothened plots of 6 representative genes/ probe sets generated by Q-PCR (red) and GeneChip (blue). AhR (arylhydrocarbon receptor, 1450695_at) showed imperfect correspondence. Cyp1a1 (cytochrome P450, family 1, subfamily a, polypeptide 1, 1422217_a_at) and Cyp1a2 (1450715_at) showed good correlations between Q-PCR and GeneChip except for the saturation in GeneChips above c. 400 copies per cell. Cyp1b1 (1416612_at) and Cyp7a1 (1422100_at) showed good correspondence. Hspa1a (heat shock protein 1A, 1452888_at) showed fair correspondence despite low copy numbers, near the nominal detection limit of the Affymetrix GeneChip system.