nucleic acid labeling protocol
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Apart from ZHTc6 cells (which were treated with 1000ng/ml of Doxycyclin to maintain cells in the Oct4+/- state), all cell lines were grown under the same conditions with no special treatment.
nucleic acid extraction protocol
RNA was extracted with RNeasy Mini kit from Qiagen (Cat. No. 74104). Quality control was performed with Agilent Bioanalyser.
Mouse ES cells were grown in GMEMB/10% FCS with 100units/ml LIF on gelatinised tissue culture flasks.