Specific usage of nuclear factors during discrete phases of ES cell differentiation during development of pluripotent stem cells to developmental zones and embryonic tissues is not completely understood. We measured total transcription in the inner cell mass (ICM) and the trophectoderm (TE) of the human embryo to understand the mechanisms underlying TE commitment. We describe here discovery of Nr5a2 as a lineage commitment factor in embryonic stem cells in the trophectoderm of the human embryo.