Fig. 1.

Experimental design. (A) Flank s.c. and intraabdominal (epididymal) white adipose tissue were taken from 6- to 7-week-old pooled C57BL/6 males. SVF and adipocytes were isolated after collagenase digestion of adipose tissues. Equal quantities of RNA were isolated from isolated adipocytes and SVF of each fat depot. A hybridization mixture containing 15 μg of biotinylated cRNA, adjusted for possible carryover of residual total RNA, was prepared and hybridized to mouse Affymetrix U74Av2 chips. (B) Among the 12,488 probe sets present on the U74Av2 chip, 8,017 probe sets representing 6,174 are annotated for Gene Ontology Biological Process. Significant genes with differential expression in both depots were identified by selecting genes that passed two independent filters of significance (P < 0.05, Student’s t test; positive false discovery rate < 0.05) (see Materials and Methods). The first filter (P < 0.05, Student’s t test) selected 1,276 genes differentially expressed in the SVF, 537 genes differentially expressed in isolated adipocytes, and 233 genes differentially expressed in both cell fractions. Of these 233 genes, 197 genes passed the second filter of significance (positive false discovery rate < 0.05) and were assessed against an a priori set of 198 annotated genes involved in embryonic development and pattern specification (see Materials and Methods). Twelve genes from this set were found among the differentially expressed genes.