Abstract:
: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.
journal_name
Nat Medjournal_title
Nature medicineauthors
Slyper M,Porter CBM,Ashenberg O,Waldman J,Drokhlyansky E,Wakiro I,Smillie C,Smith-Rosario G,Wu J,Dionne D,Vigneau S,Jané-Valbuena J,Tickle TL,Napolitano S,Su MJ,Patel AG,Karlstrom A,Gritsch S,Nomura M,Waghray A,Godoi
10.1038/s41591-020-0844-1subject
Has Abstractpub_date
2020-05-01 00:00:00pages
792-802issue
5eissn
1078-8956issn
1546-170Xpii
10.1038/s41591-020-0844-1journal_volume
26pub_type
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