Journal
NATURE MEDICINE
Volume 26, Issue 5, Pages 792-+Publisher
NATURE RESEARCH
DOI: 10.1038/s41591-020-0844-1
Keywords
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Funding
- NCI, National Institutes of Health [HHSN261100039, HHSN261201500003I]
- 'START: Standardization of Single-Cell and Single-Nucleus RNA-Seq Protocols for Tumors' project from the Chan Zuckerberg Initiative
- Klarman Cell Observatory
- EMBO Long-Term Fellowship [ALTF 738-2017]
- Kay Kendall Leukaemia Fund
- NIH/NCI [K08CA222663, CA225088]
- Burroughs Wellcome Fund Career Award for Medical Scientists
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Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.
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