A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

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…

• HH
  Howard Hughes Medical Institute
• UD
  U.S. Department of Health and Human Services

  Award: HHSN261201500003I
• A
  Amgen
• BS
  Bristol-Myers Squibb
• P
  Pfizer
• S
  Sanofi
• LA
  Leukemia and Lymphoma Society
• FN
  Frederick National Laboratory for Cancer Research

  Award: HHSN261201500003I
• BI
  Broad Institute
• CZ
  Chan Zuckerberg Initiative
• L
  Leidos
• RT
  Relay Therapeutics
• CT
  Compass Therapeutics
• KK
  Kay Kendall Leukaemia Fund
• NI
  National Institutes of Health

  Awards: K08CA222663, CA225088, HHSN261201500003I
• G
  Genentech
• ES
  EMD Serono
• KC
  Klarman Cell Observatory, Broad Institute
• P
  Pharmacyclics
• NC
  National Cancer Institute

  Awards: K08CA222663, HHSN261100039, HHSN261201500003I