Cell culture
Cell lines were maintained in culture as previously described (11). Care was taken to ensure maximum viability of cells when taken for experiments. The primary thymocytes used for Figure 2 were prepared by gentle physical disassociation of a whole thymus gland into PBS supplemented with 2% FCS. Cells were filtered to ensure that a single-cell suspension was taken forward for nuclei isolation. Human embryonic stem cells (hES) were grown in chemically defined media in the presence of Activin and FGF2, as detailed previously (33). In these conditions, hES cells remain homogenously undifferentiated.