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A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Slyper, Michal; Porter, Caroline B M; Ashenberg, Orr; Waldman, Julia; Drokhlyansky, Eugene; Wakiro, Isaac; Smillie, Christopher; Smith-Rosario, Gabriela; Wu, Jingyi; Dionne, Danielle; Vigneau, Sébastien; Jané-Valbuena, Judit; Tickle, Timothy L; Napolitano, Sara; Su, Mei-Ju; Patel, Anand G; Karlstrom, Asa; Gritsch, Simon; Nomura, Masashi; Waghray, Avinash; Gohil, Satyen H; Tsankov, Alexander M; Jerby-Arnon, Livnat; Cohen, Ofir; Klughammer, Johanna; Rosen, Yanay; Gould, Joshua; Nguyen, Lan; Hofree, Matan; Tramontozzi, Peter J; Li, Bo; Wu, Catherine J; Izar, Benjamin; Haq, Rizwan; Hodi, F Stephen; Yoon, Charles H; Hata, Aaron N; Baker, Suzanne J; Suvà, Mario L; Bueno, Raphael; Stover, Elizabeth H; Clay, Michael R; Dyer, Michael A; Collins, Natalie B; Matulonis, Ursula A; Wagle, Nikhil; Johnson, Bruce E; Rotem, Asaf; Rozenblatt-Rosen, Orit; Regev, Aviv.
Afiliação
  • Slyper M; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Porter CBM; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Ashenberg O; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Waldman J; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Drokhlyansky E; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Wakiro I; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Smillie C; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Smith-Rosario G; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
  • Wu J; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Dionne D; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Vigneau S; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Jané-Valbuena J; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Tickle TL; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
  • Napolitano S; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Su MJ; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Patel AG; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Karlstrom A; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
  • Gritsch S; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Nomura M; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Waghray A; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Gohil SH; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Tsankov AM; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
  • Jerby-Arnon L; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Cohen O; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Klughammer J; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
  • Rosen Y; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
  • Gould J; Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
  • Nguyen L; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
  • Hofree M; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Tramontozzi PJ; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Li B; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Wu CJ; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Izar B; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
  • Haq R; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Hodi FS; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Yoon CH; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Hata AN; Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Baker SJ; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Suvà ML; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Bueno R; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Stover EH; Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.
  • Clay MR; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Dyer MA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Collins NB; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Matulonis UA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Wagle N; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Johnson BE; Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA.
  • Rotem A; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Rozenblatt-Rosen O; Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Regev A; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Nat Med ; 26(5): 792-802, 2020 05.
Article em En | MEDLINE | ID: mdl-32405060
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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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Algoritmos / Núcleo Celular / Genômica / Análise de Célula Única / RNA-Seq / Neoplasias Tipo de estudo: Evaluation_studies / Guideline Limite: Adult / Animals / Child / Female / Humans Idioma: En Ano de publicação: 2020 Tipo de documento: Article
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Algoritmos / Núcleo Celular / Genômica / Análise de Célula Única / RNA-Seq / Neoplasias Tipo de estudo: Evaluation_studies / Guideline Limite: Adult / Animals / Child / Female / Humans Idioma: En Ano de publicação: 2020 Tipo de documento: Article