Comparative study of gene expression in lower and upper first molar cap stage tooth germs of DUHi and FVB mice

The dataset aims at comparing gene expression in the developing lower and upper first molars of two mouse strains: DUHi and FVB. We studied molar tooth germ an early cap stage, looking for differences in activation-inhibition mechanisms that promote tooth formation. 19202 genes are in common between FVB and reference strain C57B6 and have a MGI annotation. Out of these genes, 2234 genes (11.6%) presented a significant difference of expression between the mapping on the reference strain C57B6 and the mapping on FVB strain (DESeq2, adjusted P value < 0.05, considering the mapping effect that is with 12 replicates). This is presumably a mapping artifact, due to the sequence divergence between mouse strains. These genes were removed, and the remaining 16,968 genes were retained for further analysis. 3619 genes were found to be differentially expressed between the two strains in the lower and upper molar (?jaw+strain) Overall design: The dataset comprises 3 samples per condition: lower FVB germ, upper FVB germ, lower DUHi germ, upper DUHi germ. For each strain, we obtained 3 embryos taken from the same litter and ordered according to their body weight: 196, 219 and 239mg for DUHi embryos, 195, 215 and 233 mg for FVB embryos. Lower and upper molar germs were taken from the same embryo. Thus, we have 3 replicates for each condition. These replicates can also be viewed as tight timeseries. 3619 genes were found to be differentially expressed between the two strains in the lower and upper molar (?jaw+strain)