Rotem is a consultant and equity holder in Celsius Therapeutics. is a founder and member of the scientific advisory board of Neon Therapeutics and receives research funding from Pharmacyclics. Regev are co-inventors on patent applications filed by the Broad Institute for inventions relating to work in this manuscript, such as in PCT/US2018/060860 and US provisional application no. Regev is a founder of and equity holder in Celsius Therapeutics, an equity holder in Imunitas, and a SAB member of Syros Pharmaceuticals, Thermo Fisher Scientific, Asimov and NeoGene Therapeutics. 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.Ī. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. Each requires customization to different tissue and tumor types, posing a barrier to adoption. 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. genomics is essential to chart tumor ecosystems. 29 Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. 28 Howard Hughes Medical Institute, Chevy Chase, MD, USA. 27 Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA. 26 Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.25 Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA.24 Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.23 Howard Hughes Medical Institute, Chevy Chase, MD, USA.22 Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA.21 Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.20 Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA.19 Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA.18 Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA.17 Ludwig Center for Cancer Research at Harvard, Boston, MA, USA.16 Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.15 Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA.14 Harvard Medical School, Boston, MA, USA.13 Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.12 Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.11 Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA.10 Icahn School of Medicine at Mount Sinai, New York, NY, USA.9 Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.8 Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.7 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.6 Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.5 Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.4 Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.3 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.2 Broad Institute of Harvard and MIT, Cambridge, MA, USA.1 Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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