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1826212047911649280
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MIT
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| description |
© 2020, The Author(s). 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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| first_indexed |
2024-09-23T15:15:38Z
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Article
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| id |
mit-1721.1/136285
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| institution |
Massachusetts Institute of Technology
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| language |
English
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| last_indexed |
2024-09-23T15:15:38Z
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| publishDate |
2021
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| publisher |
Springer Science and Business Media LLC
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dspace
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| spelling |
mit-1721.1/1362852022-10-02T01:44:23Z A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors © 2020, The Author(s). 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. 2021-10-27T20:34:42Z 2021-10-27T20:34:42Z 2020 2021-07-22T15:15:20Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/136285 en 10.1038/S41591-020-0844-1 Nature Medicine Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature
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| spellingShingle |
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
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| title |
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
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| 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
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| title_full_unstemmed |
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
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| 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
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| url |
https://hdl.handle.net/1721.1/136285
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