Indirect combustion noise, generated by the acceleration and distortion of entropy waves through the turbine stages, has been shown to be the dominant noise source of gas turbines at low-frequencies and to impact the thermoacoustic behavior of the combustor. In the present work, indirect combustion noise generation is evaluated in the realistic, fully 3D transonic high-pressure turbine stage MT1 using large eddy simulations (LESs). An analysis of the basic flow and the different turbine noise generation mechanisms is performed for two configurations: one with a steady inflow and a second with a pulsed inlet, where a plane entropy wave train at a given frequency is injected before propagating across the stage generating indirect noise. The noise is evaluated through the dynamic mode decomposition (DMD) of the flow field. It is compared with the previous 2D simulations of a similar stator/rotor configuration, as well as with the compact theory of Cumpsty and Marble. Results show that the upstream propagating entropy noise is reduced due to the choked turbine nozzle guide vane. Downstream acoustic waves are found to be of similar strength to the 2D case, highlighting the potential impact of indirect combustion noise on the overall noise signature of the engine.