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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 an...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Nature Publishing Group US
2020
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7220853/ https://www.ncbi.nlm.nih.gov/pubmed/32405060 http://dx.doi.org/10.1038/s41591-020-0844-1 |
| _version_ | 1783533247797395456 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Slyper, Michal |
| collection | PubMed |
| description | 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. |
| format | Online Article Text |
| id | pubmed-7220853 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2020 |
| publisher | Nature Publishing Group US |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-72208532020-05-15 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 Nat Med Resource 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. Nature Publishing Group US 2020-05-11 2020 /pmc/articles/PMC7220853/ /pubmed/32405060 http://dx.doi.org/10.1038/s41591-020-0844-1 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
| spellingShingle | Resource 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 A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors |
| title | A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors |
| title_full | A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors |
| title_fullStr | A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors |
| title_full_unstemmed | A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors |
| title_short | A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors |
| title_sort | single-cell and single-nucleus rna-seq toolbox for fresh and frozen human tumors |
| topic | Resource |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7220853/ https://www.ncbi.nlm.nih.gov/pubmed/32405060 http://dx.doi.org/10.1038/s41591-020-0844-1 |
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