I am trying to optimize all possible ways for a high throughput screening using siRNA and dsDNA TAG (inert DNA). The experiment aims at pooling PC3 cells with a common phenotype using FACS and sequence for dsDNA TAGs to confirm the siRNA cluster involved in inducing the phenotype used for screening. In order to avoid false positives in my screening I need to know the true copy number for each TAG from the pooled cells via the FACS. Is there any sequencing technology that gives copy number along with sequence details. The TAG length is about 33bp and I will be highly obliged for your valuable suggestions on this query.
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