For microarray experiments we used one wildtype and two independent Bptf mutant cell lines in 3 culture conditions (LIF+, LIF−, and RA+). Experiments were carried out with 3 biological replications. At the day 3, Triazole (1 ml/well; Invitrogen, USA) was added to the well and total RNAs were extracted using Phase lock gel columns (Eppendorf/Brinkman) according to the manufacturer's protocol. Total RNAs were precipitated with isopropanol, washed with 70% ethanol, and dissolved in DEPC-treated H2O. 2.5 g of total RNA samples were labeled with Cy3-CTP using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA). A reference target (Cy5-CTP-labeled) was prepared from the Universal Mouse Reference RNA (Stratagene, USA). Labeled targets were purified using an RNeasy Mini Kit (Qiagen, USA) according to the Agilent's protocol, quantified by a NanoDrop scanning spectrophotometer (NanoDrop Technologies, USA), and hybridized to the NIA Mouse 44K Microarray v2.2 (whole genome 60-mer oligo; manufactured by Agilent Technologies, #014117) [68]. Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray according to the Agilent protocol (G4140-90030; Agilent 60-mer oligo microarray processing protocol - SSC Wash, v1.0).
