Scalable, coherent many-body systems can enable the realization of previously unexplored quantum phases and have the potential to exponentially speed up information processing. Thermal fluctuations are negligible and quantum effects govern the behavior of such systems with extremely low temperature. We report the cooling of a quantum simulator with 10,000 atoms and mass production of high-fidelity entangled pairs. In a two-dimensional plane, we cool Mott insulator samples by immersing them into removable superfluid reservoirs, achieving an entropy per particle of $1.9^{+1.7}_{-0.4} times 10^{-3} k_{text{B}}$. The atoms are then rearranged into a two-dimensional lattice free of defects. We further demonstrate a two-qubit gate with a fidelity of 0.993 $pm$ 0.001 for entangling 1250 atom pairs. Our results offer a setting for exploring low-energy many-body phases and may enable the creation of large-scale entanglement
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