Exploring tissue architecture using spatial transcriptomics

Nature, Год журнала: 2021, Номер 596(7871), С. 211 - 220

Опубликована: Авг. 11, 2021

Язык: Английский

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Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

Nature Reviews Genetics, Год журнала: 2021, Номер 22(10), С. 627 - 644

Опубликована: Июнь 18, 2021

Язык: Английский

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An introduction to spatial transcriptomics for biomedical research

Genome Medicine, Год журнала: 2022, Номер 14(1)

Опубликована: Июнь 27, 2022

Abstract Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over the past decade, particularly in developmental biology, cancer, immunology, and neuroscience. Most commercially available scRNA-seq protocols require cells to be recovered intact viable from tissue. This precluded many cell types study largely destroys spatial context that could otherwise inform analyses of identity function. An increasing number platforms now facilitate spatially resolved, high-dimensional assessment gene transcription, known as ‘spatial transcriptomics’. Here, we introduce different classes method, which either record locations hybridized mRNA molecules tissue, image positions themselves prior assessment, or employ arrays probes pre-determined location. We review sizes tissue area can assessed, their resolution, genes profiled. discuss if preservation influences choice platform, provide guidance on whether specific may better suited discovery screens hypothesis testing. Finally, bioinformatic methods analysing transcriptomic data, including pre-processing, integration with existing inference cell-cell interactions. Spatial -omics are already improving our understanding human tissues research, diagnostic, therapeutic settings. To build upon these recent advancements, entry-level those seeking own research.

Язык: Английский

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Spatial omics and multiplexed imaging to explore cancer biology

Nature Methods, Год журнала: 2021, Номер 18(9), С. 997 - 1012

Опубликована: Авг. 2, 2021

Язык: Английский

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Applications of single-cell sequencing in cancer research: progress and perspectives

Journal of Hematology & Oncology, Год журнала: 2021, Номер 14(1)

Опубликована: Июнь 9, 2021

Single-cell sequencing, including genomics, transcriptomics, epigenomics, proteomics and metabolomics is a powerful tool to decipher the cellular molecular landscape at single-cell resolution, unlike bulk which provides averaged data. The use of sequencing in cancer research has revolutionized our understanding biological characteristics dynamics within lesions. In this review, we summarize emerging technologies recent progress obtained by information related landscapes malignant cells immune cells, tumor heterogeneity, circulating underlying mechanisms behaviors. Overall, prospects facilitating diagnosis, targeted therapy prognostic prediction among spectrum tumors are bright. near future, advances will undoubtedly improve highlight potential precise therapeutic targets for patients.

Язык: Английский

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Harnessing multimodal data integration to advance precision oncology

Nature reviews. Cancer, Год журнала: 2021, Номер 22(2), С. 114 - 126

Опубликована: Окт. 18, 2021

Язык: Английский

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Understanding 3D genome organization by multidisciplinary methods

Nature Reviews Molecular Cell Biology, Год журнала: 2021, Номер 22(8), С. 511 - 528

Опубликована: Май 5, 2021

Язык: Английский

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The emerging landscape of spatial profiling technologies

Nature Reviews Genetics, Год журнала: 2022, Номер 23(12), С. 741 - 759

Опубликована: Июль 20, 2022

Язык: Английский

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The expanding vistas of spatial transcriptomics

Nature Biotechnology, Год журнала: 2022, Номер 41(6), С. 773 - 782

Опубликована: Окт. 3, 2022

Язык: Английский

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The dawn of spatial omics

Science, Год журнала: 2023, Номер 381(6657)

Опубликована: Авг. 3, 2023

Spatial omics has been widely heralded as the new frontier in life sciences. This term encompasses a wide range of techniques that promise to transform many areas biology and eventually revolutionize pathology by measuring physical tissue structure molecular characteristics at same time. Although field came age past 5 years, it still suffers from some growing pains: barriers entry, robustness, unclear best practices for experimental design analysis, lack standardization. In this Review, we present systematic catalog different families spatial technologies; highlight their principles, power, limitations; give perspective suggestions on biggest challenges lay ahead incredibly powerful-but hard navigate-landscape.

Язык: Английский

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