作者
Michal Slyper, Caroline BM Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Dionne, Sébastien Vigneau, Judit Jané-Valbuena, Timothy L Tickle, Sara Napolitano, Mei-Ju Su, Anand G Patel, Asa Karlstrom, Simon Gritsch, Masashi Nomura, Avinash Waghray, Satyen H Gohil, Alexander M Tsankov, Livnat Jerby-Arnon, Ofir Cohen, Johanna Klughammer, Yanay Rosen, Joshua Gould, Lan Nguyen, Matan Hofree, Peter J Tramontozzi, Bo Li, Catherine J Wu, Benjamin Izar, Rizwan Haq, F Stephen Hodi, Charles H Yoon, Aaron N Hata, Suzanne J Baker, Mario L Suvà, Raphael Bueno, Elizabeth H Stover, Michael R Clay, Michael A Dyer, Natalie B Collins, Ursula A Matulonis, Nikhil Wagle, Bruce E Johnson, Asaf Rotem, Orit Rozenblatt-Rosen, Aviv Regev
发表日期
2020/5/1
期刊
Nature medicine
卷号
26
期号
5
页码范围
792-802
出版商
Nature Publishing Group US
简介
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 …
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M Slyper, CBM Porter, O Ashenberg, J Waldman… - Nature medicine, 2020