The present disclosure describes methods and systems for use in the production of adeno-associated virus (AAV) particles and AAV formulations, including recombinant adeno-associated virus (rAAV) particles and formulations. In certain embodiments, the present disclosure presents methods and systems for clarifying, purifying, formulating, filtering and processing AAV particles and AAV formulations. The present disclosure also describes compositions, methods and processes for the design, preparation, manufacture, use and/or formulation of AAV particles comprising modulatory polynucleotides, e.g., polynucleotides encoding small interfering RNA (siRNA) molecules which target the Huntingtin (HTT) gene (e.g., the wild-type or the mutated CAG-expanded HTT gene). Methods for using formulated AAV particles comprising modulatory polynucleotides to inhibit the HTT gene expression in a subject with a eurodegenerative disease (e.g., Huntington' s Disease (HD)) are also disclosed.