(A) Clonal lines derived from CBD total lysate had two distinct inclusion patterns, CBD1(t), CBD2(t). Clonal lines derived from CBD Ms had two patterns identical to those from the total lysate, CBD1(m), CBD2(m), and a third, CBD3(m). (B) RD-YFP from CBD1(t) and CBD1(m) had mixed solubility. In CBD2(t) and CBD2(m), most RD-YFP was present in the supernatant. CBD3(m) had mixed solubility with most RD-YFP in the insoluble fraction. Total (T) lysate was resolved into supernatant (S) and pellet (P) fractions by ultracentrifugation. Supernatant to pellet ratio loaded on the gel was 1:1 for all samples. Lane 1 represents DS1, which is comprised of RD-YFP monomer that is completely digested. (C) RD-YFP aggregates from CBD1(t) and CBD1(m) exhibited similar patterns of proteolysis, with protease-resistant bands around 10–15 kD and a strong band around 15 kD. Proteolysis of RD-YFP from CBD2(t) and CBD2(m) only produced a strong band around 15 kD. CBD3(m) had a unique proteolysis pattern with a band around 10–15 kD. (D) Lysates from clones CBD1(t), CBD1(m), CBD2(t) and CBD2(m) had similar seeding profiles, while lysate from CBD3(m) had more potent seeding activity. Images are representative of thousands similar cells. Western blots are representative of at least three replicates. Seeding assays represent an individual experiment in which each data point represents a sample analyzed in triplicate. Error bars represent the standard deviation.