We selected protein coding gene controls consisting of both transcription factors and chromatin proteins. These proteins were selected based on their well-characterized role in regulating mouse ES cells and include Pou5f1 (Oct4)35,48, Sox217,49, Nanog29,30, Stat350, Klf451, and Zfp42 (Rex1)52. In addition, we selected additional transcriptional and chromatin regulators that were identified by RNAi screens as regulators of pluripotency17,20,23 and/or were found in smaller focused studies to have critical roles in the maintenance of the pluripotent state (such as Carm153, Chd154, Thap1155, Suz1218,19,36, and Setdb121,56). A full list is provided in Supplemental Table 2.
