This study describes the transcriptome profiling of: 1) Mll1fl/fl mESCs in LIF/Serum medium as control; 2) VD3 and MM-401 (Mll1i) treated mESCs in LIF/serum medium ; 2) VD3 treated mESCs in LIF/serum medium. Overall design: RNA-Seq profiling on mouse pluripotent cells. Biological duplicates of each sample are labled as rep1/2.