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High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE.
Vahid, Milad R; Brown, Erin L; Steen, Chloé B; Zhang, Wubing; Jeon, Hyun Soo; Kang, Minji; Gentles, Andrew J; Newman, Aaron M.
Afiliación
  • Vahid MR; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
  • Brown EL; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
  • Steen CB; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
  • Zhang W; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
  • Jeon HS; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
  • Kang M; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
  • Gentles AJ; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
  • Newman AM; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
Nat Biotechnol ; 41(11): 1543-1548, 2023 Nov.
Article en En | MEDLINE | ID: mdl-36879008
ABSTRACT
Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Perfilación de la Expresión Génica / Transcriptoma Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Perfilación de la Expresión Génica / Transcriptoma Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos