A large-scale application of the “stacked modeling” approach for chromatin state discovery previously provides a single “universal” chromatin state annotation of thehumangenome based jointly on data from many cell and tissue types. Here, we produce an analogous chromatin state annotation formousebased on 901 datasets assaying 14 chromatin marks in 26 cell or tissue types. To characterize each chromatin state, we relate the states to external annotations and compare them to analogously definedhumanstates. We expect the universal chromatin state annotation formouseto be a useful resource for studying this key model organism’s genome.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13059-023-02994-x.