Transition of the long-term infection culture through the aggregation phase again recapitulated many reported features of Mtb infection, such as the production of several key cytokines (TNF-α, IL-1α/β, IL-10; Supplementary Figure 3A-3D) and chemokines (IL-8, MIP-1α/β, and MCP-1; Supplementary Figure 3E-3H) involved in host cell responses to Mtb infection. The gene discussed is CCL2; the disease is infection.