We chose a microarray approach to investigate any differentiation defects of Bptf knockout ES cells in undifferentiated and early differentiation states. Differentiation was induced by LIF withdrawal (LIF−) or retinoic acid (RA) for three days before harvesting RNA. A comparison of Bptf-dependent genes by Venn diagram and manual clustering identifies six categories; those being affected under only one of the growth conditions (LIF+, LIF− or RA Regulation), those being affected in all three conditions (Constitutive Regulation), a class of genes which were regulated in the same direction in two of three conditions (Complex Regulation) and genes with mixed dependence (Mixed Regulation) (Figure 4A and 4B) (Dataset S1).
