STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging
Single-cell RNA sequencing has revolutionized our understanding of cellular diversity but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (single-cell transcriptomics analysis and multimodal profiling), a highly scalable approach for the profiling of single cells. By leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, enabling cost-efficient single-cell genomics of millions of cells. Immobilizing (stamping) cells in suspension onto imaging slides, STAMP supports multimodal (RNA, protein, and H&E) profiling, while retaining cellular structure and morphology. We demonstrate STAMP's versatility by profiling peripheral blood mononuclear cells, cell lines, and stem cells. We highlight the capability of STAMP to identify ultra-rare cell populations, simulate clinical applications, and show its utility for large-scale perturbation studies. In total, we present data for 10,962,092 high-quality cells/nuclei and 6,030,429,954 transcripts. STAMP makes high-resolution cellular profiling more accessible, scalable, and affordable.
Authors
- Jasmine Plummer (ORCID: https://orcid.org/0000-0001-7263-350X)
- Monika Mohenska
- Adrienne E. Sullivan (ORCID: https://orcid.org/0000-0003-3967-892X)
- B. Kate Dredge (ORCID: https://orcid.org/0000-0002-6103-5165)
- Maycon Marção (ORCID: https://orcid.org/0000-0003-1320-6588)
- Luciano G. Martelotto (ORCID: https://orcid.org/0000-0002-9625-1183)
- Helena L. Crowell (ORCID: https://orcid.org/0000-0002-4801-1767)
- Ginevra Caratù (ORCID: https://orcid.org/0000-0003-1085-8062)
- Juan C. Nieto (ORCID: https://orcid.org/0000-0002-3400-1488)
- Elise T. Courtois (ORCID: https://orcid.org/0000-0002-8749-2719)
- German Atzin Mora-Roldan (ORCID: https://orcid.org/0000-0002-0237-7472)
- Yutian Liu (ORCID: https://orcid.org/0000-0001-6932-5207)
- William F. Flynn (ORCID: https://orcid.org/0000-0001-6533-0340)
- Holger Heyn (ORCID: https://orcid.org/0000-0002-3276-1889)
- Raymond K. H. Yip (ORCID: https://orcid.org/0000-0003-2698-7686)
- Anna Pascual Reguant (ORCID: https://orcid.org/0000-0002-5042-3699)
- Irepan Salvador‐Martínez (ORCID: https://orcid.org/0000-0002-3188-9784)
- Santhosh Sivajothi (ORCID: https://orcid.org/0000-0002-8854-4517)
- Kellie Wise (ORCID: https://orcid.org/0009-0005-8937-4352)
- Ruvimbo D Mishi (ORCID: https://orcid.org/0000-0002-8166-1155)
- Emily Soja (ORCID: https://orcid.org/0009-0009-8207-9683)
- Hannah Chasteen
- María Teresa Gil Ruiz (ORCID: https://orcid.org/0000-0001-5132-9824)
- Emanuele Pitino (ORCID: https://orcid.org/0000-0002-1726-5924)
- Felipe Segato-Dezem
- J. M. Polo
- Mohmed Abdalfttah (ORCID: https://orcid.org/0000-0002-8294-2979)
Institutions
- St. Jude Children's Research Hospital (US)
- Walter and Eliza Hall Institute of Medical Research (AU)
- Spanish National Cancer Research Centre (ES)
- Jackson Laboratory (US)
- Centre for Cancer Biology (AU)
- Centro Nacional de Análisis Genómico (ES)
- The University of Adelaide (AU)
Publication Details
- Journal
- Cell
- Published
- 2025-06-17
- DOI
- https://doi.org/10.1016/j.cell.2025.05.027
- Citations
- 15
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 12.09