DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). Nuclei isolated from 3T3-L1 cells four hours after induction of differentiation were subjected to DNase I digestion and small fragments were isolated by running the digested DNA through a sucrose gradient. DNA of approximately 100-150 bp were sequenced on the Illumina platform according to the instructions of the manufacturer. All this data comes from extensive sequencing of our previously published DHS-seq library (Siersbæk et al., 2011, EMBO J, 30(8):1459-72) and these data were therefore combined with our previously published data for downstream analyses, including identification of the DHS sites and footprints found here as processed data files.