Comparative Transcriptomic Analysis of Fibroblasts

Gene expression profiles of fibroblast cell lines derived from day 27 control and parthenogenetic embryos were compared in each of the three platforms. For each platform, three biological replicates were used. Each biological replicate consisted of fibroblasts derived from a randomly selected fetus and cultured for two passages. One of the biological replicate was further split into three technical replicates. For biparental controls, sex of fetuses was determined by PCR and only female fetuses were used to avoid sex-related gene expression differences. For the technical replicates, one of the biological replicates was split into three identical pools of RNA and hybridized independently. For cross-platform comparisons, the same starting pool of total RNA was used to generate labeled targets for each of the three individual experiments. A balanced dye swap design was employed for the two-channel glass oligonucleotide microarray and one control and one parthenogenetic biological replicate were each divided into three technical replicates (Figure 6).