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Experimental methods for testing enhancer activity. Methods that are used to assess enhancer activity involve a trade-off between the number of sequences that can be tested and the number of cells assessed at one time. Developmental transgenic approaches can reveal enhancer activity across many cells at the same time on a per sequence basis. On the other hand, massively parallel reporter assays (MPRA) are able to assay thousands of sequences by random integration or in an episomal manner. Perturbation experiments using CRISPR interference (CRISPRi) can reveal transcriptional targets and can be combined with single-cell readouts to increase throughput

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