De-CIPHER-Ing Transcriptomes and Proteins Together with New RNA-Seq Technology

Key Takeaways

• CIPHER-seq quantifies RNA and intracellular proteins in single cells
• Protocol reduces mitochondrial stress compared with standard intracellular staining
• Accurately captures cytokine induction timing in stimulated PBMCs
• Matches cell-type recovery of existing Proteintech method
• Provides high‑quality transcriptomes for cancer and inflammation research

Pulse Analysis

Single‑cell technologies have reshaped biomedical discovery, yet most approaches capture either gene expression or surface proteins, leaving a critical blind spot for intracellular signaling molecules such as cytokines. Traditional intracellular staining, optimized for flow cytometry, often compromises RNA integrity or induces stress responses that skew sequencing results. CIPHER‑seq bridges this gap by marrying a gentle fixation chemistry with RNase‑protective conditions, allowing researchers to profile the full transcriptome while directly measuring intracellular protein levels in the same cell.

In head‑to‑head tests, CIPHER‑seq performed on par with the industry‑standard Proteintech protocol for immune‑cell recovery, but it generated markedly lower mitochondrial stress signatures—a key quality metric for single‑cell RNA‑seq. When applied to peripheral blood mononuclear cells stimulated with PMA/ionomycin, the platform resolved the sequential activation of IFNG RNA followed by its protein product, mirroring the biological lag between transcription and translation. This temporal resolution, visualized through UMAP clustering and pseudotime analysis, offers researchers a granular view of cytokine dynamics that was previously inferred only indirectly.

The ability to capture both transcriptomic and intracellular protein landscapes in real time has immediate implications for oncology and inflammatory disease research. By revealing exactly when immune cells produce pro‑ or anti‑tumor cytokines, CIPHER‑seq can inform the selection of patients most likely to respond to checkpoint inhibitors or cytokine‑based therapies. Moreover, its compatibility with existing single‑cell pipelines means laboratories can adopt the technology without overhauling infrastructure, accelerating translational studies that aim to convert molecular insights into next‑generation therapeutics.