Fig. 1

Comparative transcriptome analysis of embryos subjected to different technologies and controls (no treatment). A Principal Component analysis (PCA) based on the 500 genes with the highest variation of expression levels in the data set (vitrified embryos: VIT in blue; in vitro culture embryos: IVC in orange; and in vivo fresh control embryos: CO in black). B–D Dendrograms representing results of unsupervised hierarchical clustering (HCL) created with Pearson correlation coefficient by MeV. Rows show differentially expressed genes (DEGs) (cut off FDR 0.001) while columns represent embryo samples subjected to different technologies or controls B: VIT vs. IVC; C: IVC vs. CO and D: VIT vs. CO). Each sample represents a pool of embryos. Mean–centered expression values (log2 counts per million of sample–mean of log2 CPM of all samples) for the samples of the three embryo groups. Color scale is from − 3 (blue, lower than mean) to 3 (red, higher than mean). E–G Percentage of up– and downregulated genes according to different log2FC cut–offs in VIT vs. IVC embryos E, IVC vs. CO embryos F, and VIT vs. CO embryos G