Technical and biological sources of noise confound multiplexed enhancer AAV screening.

All enhancers maintained high specificity for their intended cell type target, with a small trend towards lowered specificity with nuclear mBC constructs (Welch two sample t-test: P = 0.096; mean ± standard deviation: 86 ± 13% (mBC nuclear constructs) compared to 92 ± 10% (original constructs), Fig. 1m ), possibly due to better detection of weakly (often off-target) expressing cells resulting from the higher signal-to-background ratio of the nuclear reporter compared to the cytosolic reporter (insets of Fig. 1e–g, i–k ).

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However, we only observed a modest correlation between protein and UMIs that did not reach statistical significance (Pearson’s r , Individual Preps: r = 0.532, P = 0.28; Pooled Preps: r = 0.500, P = 0.31, Supplementary Fig. 6i ).

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