Evaluation of Hox gene expression in wild-type and mutant c-Kit⁺ FL cells. Expression of Hox genes in c-Kit⁺ FL cells derived from 6 to 8 E14.5 FLs from littermates (wt) or from mutant embryos of different litters was evaluated by QRT-PCR. Analysis was carried out in triplicate on cDNA from total RNA, and data processing was done as described by Thompson et al.24 (A) Expression of Hoxb genes in wild-type FL cells in copy numbers, ordered according to the highest levels of RNA copies per 0.05 μg cDNA. Values below 10 copies were considered as not expressed. Fold difference in expression of the complete set of Hox genes in c-Kit⁺ cells of Hoxb4^-/- (B) and Hoxb1-b9^-/- (C) FLs. Two sets of independent data were generated for wild-type FL cells. Hox gene expression in KO FL cells was compared to both data sets. For genes that showed more that a 3-fold change in expression, a second independent experiment was performed. The bar graph includes the fold difference of both values for mutant cells (when available) compared to both independent data sets of wild-type cells. Amplitudes of changes in expression determined by comparison of various data sets are indicated by different colors. Note that no expression was detected for Hoxb4 and Hoxb1 to Hoxb9 in the Hoxb4 and Hoxb1-b9 mutants. Of all 39 clustered Hox genes, no appreciable values were obtained for Hoxc12,-c13,-d1,-d8,-d10,-d11,-d12, and -d13 in the Hoxb4 mutant and for Hoxc12 and -d1 in Hoxb1-Hoxb9^-/- cells.