Abstract Single-cell RNA sequencing inadequately predicts protein abundance, particularly for intracellular cytokines. We developed CIPHER-seq (Cytokine Intracellular Protein High-throughput Expression with RNA-sequencing), enabling simultaneous quantification of intracellular proteins and transcriptomes. This system provides five layers of analysis. CIPHER-seq matched commercial protocols in immune cell recovery while significantly reducing mitochondrial stress signatures. Applied to stimulated PBMCs, CIPHER-seq resolved robust cytokine induction and metabolic remodeling, establishing a streamlined platform for intracellular multimodal profiling.
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Avni M. Bhalgat
Katarina Micin
Maurizio Affer
Scientific Reports
University of California, San Francisco
University of Miami
Florida International University
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Bhalgat et al. (Wed,) studied this question.
www.synapsesocial.com/papers/69d895ea6c1944d70ce071b2 — DOI: https://doi.org/10.1038/s41598-026-44946-y