Table 1.

The soaking extract method and its modifications for control experiments in this report

Step #	Steps in standard protocol	Modifications of standard protocol for the specified control experiments, and relevant figure number
1	Frozen tissue thawed, grey matter dissected	Fig S3I–L: Fresh tissue
2	Tissue chopped using McIlwain Tissue Chopper set to 0.5 mm width
3	Tissue bits soaked in 1:5 w:v extraction buffer 30 min 4°C with nutation in 50-ml tube	Fig S2B: Tissue bits first rinsed with ~15 volumes extraction buffer before soaking Fig S3E: 1:15 w:v
4	2,000 g fixed angle (pelleting distance ~4 cm) 10 min 4°C, top 90% supernatant collected
5	200,000 g in SW41Ti (pelleting distance ~9 cm) 110 min 4°C, top 90% of supernatant collected	Fig S2A: Top 90% of supernatant divided into top 2 ml and bottom ~7 ml Fig 1C–G: 20,000 – 475,000 g in TLA100.3 (pelleting distance ~2 cm) for 110 min 4°C; top 90% of supernatant collected
6	Aliquot 1 ml into 1.5-ml Eppendorf LoBind tubes; store −80°C	Fig S2E: Aliquot into siliconized or BSA-coated tubes Fig S3C, H: Store at 4°C Fig S3D: Dilute serially before freezing Fig S3E–F: Add various Aβ aggregation inhibitors before freezing Fig S3G: Filter through aluminum oxide filters before freezing
7 (re-centrifugation)	Thaw aliquot(s), 20,000 g fixed angle (pelleting distance ~1 cm) 60 min 4°C. Retain input, supernatant and pellet for ELISA and/or EM