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

Bibliographic Details
Title:	A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
Authors:	Slyper, Michal, Porter, Caroline, Ashenberg, Orr, Waldman, Julia, Drokhlyansky, Eugene, Wakiro, Isaac, Smilie, Christopher, Smith-Rosario, Gabriela, Wu, Jingyi, Dionne, Danielle, Vigneau, Sebastien, Jane-Valbuena, Judit, Tickle, Timothy, Napolitano, Sara, Su, Mei-Ju, Patel, Anand, Karlstrom, Asa, Gristch, Simon, Nomura, Masashi, Waghray, Avinash, Gohil, Satyen, Tsankov, Alexander, Jerby-Arnon, Livnat, Cohen, Ofir, Klughammer, Johanna, Rosen, Yanay, Gould, Joshua, Nguyen, Lan, Hofree, Matan, Tramontozzi, Peter, Levy, Rachel, Li, Bo, Wu, Catherine, Izar, Benjamin, Haq, Rizwan, Hodi, Stephen, Yoon, Charles, Hata, Aaron, Baker, Suzanne, Suva, Mario, Bueno, Raphael, Stover, Elizabeth, Clay, Michael, Dyer, M Aiven, Collins, Natalie, Matulonis, Ursula, Wagle, Nikhil, Johnson, Bruce, Rotem, Asaf, Rozenblatt-Rosen, Orit, Regev, Aviv
Source:	Slyper, Michal, Caroline Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smilie et al. "A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors." Nat Med 26, no. 5 (2020): 792-802. DOI: 10.1038/s41591-020-0844-1
Publisher Information:	Springer Science and Business Media LLC, 2020.
Publication Year:	2020
Subject Terms:	General Biochemistry, Genetics and Molecular Biology, General Medicine
More Details:	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. Version of Record
Document Type:	Journal Article
File Description:	application/pdf
Language:	English
ISSN:	1078-8956 1546-170X
Relation:	Nature Medicine; Nat Med
Access URL:	https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37377135
Accession Number:	edshld.1.37377135
Database:	Digital Access to Scholarship at Harvard (DASH)

More Details
ISSN:	10788956 1546170X
Language:	English