Total RNA was isolated from primary cells or tumors, using the RNeasy Plus Mini Kit (Qiagen) and sequenced on an Illumina HiSeq2000. At least 5000 cells were sorted  directly  in lysis buffer for specifc T cell progenitor populations in the thymus while at least 5 million cells have used for RNA isolation form thymic lymphomas. Unless otherwise indicated samples from tumors were isolated without sorting specific polulations.