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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Museum of spatial transcriptomics

Nature Methods, Год журнала: 2022, Номер 19(5), С. 534 - 546

Опубликована: Март 10, 2022

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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Methods and applications for single-cell and spatial multi-omics

Nature Reviews Genetics, Год журнала: 2023, Номер 24(8), С. 494 - 515

Опубликована: Март 2, 2023

Язык: Английский

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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

Nature Methods, Год журнала: 2021, Номер 18(11), С. 1352 - 1362

Опубликована: Окт. 28, 2021

Charting an organs’ biological atlas requires us to spatially resolve the entire single-cell transcriptome, and relate such cellular features anatomical scale. Single-cell single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for measurements, at lower resolution with limited sensitivity. Targeted in situ technologies solve both issues, are gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data various forms of collected from same region, including MERFISH, STARmap, smFISH, Transcriptomics (Visium) histological images. Tangram map any type data, multimodal as those SHARE-seq, which used reveal patterns chromatin accessibility. We demonstrate on healthy mouse brain tissue, by reconstructing genome-wide anatomically integrated visual somatomotor areas. is versatile tool aligning resolved using deep learning.

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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Microglia in Neuroinflammation and Neurodegeneration: From Understanding to Therapy

Frontiers in Neuroscience, Год журнала: 2021, Номер 15

Опубликована: Сен. 24, 2021

Microglia are the resident macrophages of central nervous system (CNS) acting as first line defense in brain by phagocytosing harmful pathogens and cellular debris. emerge from early erythromyeloid progenitors yolk sac enter developing before establishment a fully mature blood–brain barrier. In physiological conditions, during development, microglia contribute to CNS homeostasis supporting cell proliferation neural precursors. post-natal life, such cells preserving integrity neuronal circuits sculpting synapses. After injury, change their morphology down-regulate those genes homeostatic functions. However, it is still unclear whether changes accompanied molecular functional modifications that might pathological process. While comprehensive transcriptome analyses at single-cell level have identified specific gene perturbations occurring “pathological” microglia, precise protective/detrimental role neurological disorders far being elucidated. this review, results so obtained regarding neurodegenerative will be discussed. There solid sound evidence suggesting regulating functions disease pathology represent strategy develop future therapies aimed counteracting degeneration multiple sclerosis, Alzheimer’s disease, Parkinson’s amyotrophic lateral sclerosis.

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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