Data set of highly inclined and laminated optical sheet microscopy (HILOM) videos and single-molecule tracking trajectories of mouse ES cells expressing EGFP-Nanog and EGF-Oct4. Culture conditions were in the presence of 2i and LIF, in the presence of LIF, 1 day and 2 days after removal of LIF. The videos are categorized by the EGF-Oct4 expression level of EGFP-Nanog. The number of frames in one video is 2000, and two are one set: 2000 frames of 400 frames of 450, 50, 250, 100, and 150 ms and 2000 interval s of 50 ms interval