Do I need to clean up the REPLI-g amplification product for downstream analysis?

No. Dilute the amplified REPLI-g WGA product in 1x TE to a concentration identical to the gDNA concentration applied in downstream genotyping experiments. There are some residual random primers and dNTPs in the amplified mix, but these will not interfere with most genotyping methods after they are diluted. However, in some cases, purifying amplified DNA before use in a highly multiplexed PCR may yield better results.

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