Targeted single-cell RNA and perturbation sequencing with TAP-seq.

TAP-seq enables sensitive, cost-effective targeted Perturb-seq by measuring hundreds of selected transcripts per cell, yielding guide RNA assignments and differential expression of perturbation effects.

• Why it matters: Whole-transcriptome Perturb-seq needs high sequencing depth, making functional genomics screens expensive and limiting broad adoption.
• What they did: The protocol details a targeted readout workflow: choose genes, design primers, run a pilot, then perform TAP-seq and analyze single-cell guide RNA and selected transcript expression, with platform adaptation guidance.
• The result: TAP-seq produces single-cell measurements of selected gene and guide RNA levels, guide RNA-to-cell assignments, and differential expression results, and can be completed in 2 days (excluding data analysis).

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