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CIPHER-seq enables low-stress intracellular multimodal profiling of immune activation

ABSTRACT: This study introduces CIPHER-seq, an optimized intracellular CITE-seq workflow that minimizes fixation-induced cellular stress while enabling simultaneous measurement of intracellular proteins and transcriptomes in the same cell. Peripheral blood mononuclear cells (PBMCs) were processed using either CIPHER-seq or a commercial intracellular protocol (Proteintech) under unstimulated or PMA/ionomycin-stimulated conditions. Single-cell RNA and antibody-derived tag (ADT) libraries were generated using 10x Genomics Flex chemistry. The dataset enables benchmarking of intracellular chemistries, assessment of RNA–protein concordance, and characterization of cytokine-driven immune activation at single-cell resolution.

ORGANISM(S): Homo sapiens

PROVIDER: GSE314400 | GEO | 2026/04/08

REPOSITORIES: GEO

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