SPARK-seq is a high-throughput aptamer discovery and kinetic profiling platform that integrates single-cell-level mRNA and aptamer sequencing with CRISPR-based perturbation of surface proteins.[1] The platform combines CRISPR knockdown of 13 surface proteins with single-cell sequencing of gRNAs, transcriptomes, and aptamer binding events.The aptamer library has undergone four rounds of enrichment by Cell-SELEX against a pool of cells with genetic perturbations.[SPARK-seq enables simultaneous mapping of thousands of aptamer-target interactions in a native cellular context and identification of aptamers binding low-abundance targets.1[1][2] The method converts millions of aptamer binding events into high-dimensional sequencing data associated with genotype, phenotype, and ligand status.[1][1] This multimodal approach extends the dynamic range of detection of conformationally sensitive targets and supports rapid optimization of highly specific aptamers for diagnostics and therapeutics.