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The International Society for Extracellular Vesicles recommends some negative controls, such as Grp94=HSP90B1, calnexin=CANX (both ER markers), GM130 (Golgi marker), Cytochrome C (mitochondrial marker), Histones (nuclear marker), and Argonaute =AGO (RISC complex marker). See this paper for details on the ISEV's recommendations for verifying that you have EVs:
Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles.
J Extracell Vesicles. 2014 Dec 22;3:26913. doi: 10.3402/jev.v3.26913. eCollection 2014.
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