In vitro production (IVP) of cattle embryos over the past two decades has revealed several negative impacts that have been attributed to the artificial microenvironment. Studies on embryos produced in vitro clearly point to aberrant gene expression levels. So far, the causal association between phenotype and measured gene expression has not led to substantial improvement of IVP systems. The aim of this study was to generate a unique dataset composed of microarray-derived relative transcript abundance values for blastocysts produced in ten in vitro systems differing primarily in culture medium formulation. Between-group comparisons determine the level of overall similarity among systems relative to in vivo reference embryos. The use of the dataset to contrast all in vitro treatments with the in vivo blastocysts pointed to a single common gene network. The 'boutique' array contained a panel of novel uncharacterized transcripts that were variably expressed depending on the medium in which the blastocysts were produced. These novel transcripts were differentially expressed in blastocysts even as carryover from conditions encountered 7 days earlier during oocyte maturation. All of the selected novel candidates thus expressed were from intergenic regions. The function of this long non-coding RNA remains unknown but clearly points to an additional level of complexity in early embryo development.