GDNA mix AA/(AA+GG) (A) Takeda et al., Supplemental Figure 1 (C) Sequence Height A / (A+G) Sequence Height A / (A+G) Sequence Height A / (A+G) (B) (D)

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gDNA mix AA/(AA+GG) (A) Takeda et al., Supplemental Figure 1 (C) Sequence Height A / (A+G) Sequence Height A / (A+G) Sequence Height A / (A+G) (B) (D) gDNA mix AA/(AA+GG) pRL-TK-4xA/4xG mix A/(A+G) pRL-TK-3’A/3’G mix A/(A+G) GeneScan Area A / (A+G)

HLHLHLHLHLHL Sonication (A) Takeda et al., Supplemental Figure 2 InputSupIP No Fixation miRNA 11M HLHLHHLHLHL InputSupIP With Fixation * hAGOs h l Input IP HLHLHLHLSonication miRNA RT (B) 11M1 1 1 No FixationWith Fixation Log 2 [ (A/G IP ) / (A/G inp ) ]

Takeda et al., Supplemental Figure 3 Log 2 [ (A/G) / (A/G gDNA ) ] Input IP