Exploring tissue architecture using spatial transcriptomics

Nature, Journal Year: 2021, Volume and Issue: 596(7871), P. 211 - 220

Published: Aug. 11, 2021

Language: Английский

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

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(8), P. 494 - 515

Published: March 2, 2023

Language: Английский

An introduction to spatial transcriptomics for biomedical research

Genome Medicine, Journal Year: 2022, Volume and Issue: 14(1)

Published: June 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.

Language: Английский

Spatial omics and multiplexed imaging to explore cancer biology

Nature Methods, Journal Year: 2021, Volume and Issue: 18(9), P. 997 - 1012

Published: Aug. 2, 2021

Language: Английский

Understanding 3D genome organization by multidisciplinary methods

Nature Reviews Molecular Cell Biology, Journal Year: 2021, Volume and Issue: 22(8), P. 511 - 528

Published: May 5, 2021

Language: Английский

The emerging landscape of spatial profiling technologies

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(12), P. 741 - 759

Published: July 20, 2022

Language: Английский

The expanding vistas of spatial transcriptomics

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 41(6), P. 773 - 782

Published: Oct. 3, 2022

Language: Английский

The dawn of spatial omics

Science, Journal Year: 2023, Volume and Issue: 381(6657)

Published: Aug. 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.

Language: Английский

Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

Science, Journal Year: 2021, Volume and Issue: 373(6556)

Published: Aug. 12, 2021

Capturing the heterogeneous phenotypes of microbial populations at relevant spatiotemporal scales is highly challenging. Here, we present par-seqFISH (parallel sequential fluorescence in situ hybridization), a transcriptome-imaging approach that records gene expression and spatial context within microscale assemblies single-cell molecule resolution. We applied this to opportunistic pathogen Pseudomonas aeruginosa, analyzing about 600,000 individuals across dozens conditions planktonic biofilm cultures. identified numerous metabolic- virulence-related transcriptional states emerged dynamically during growth, as well spatially resolved metabolic heterogeneity sessile populations. Our data reveal distinct physiological can coexist same just several micrometers away, underscoring importance microenvironment. results illustrate complex dynamics new way studying them high

Language: Английский

Spatial epigenome–transcriptome co-profiling of mammalian tissues

Nature, Journal Year: 2023, Volume and Issue: 616(7955), P. 113 - 122

Published: March 15, 2023

Abstract Emerging spatial technologies, including transcriptomics and epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context 1–5 . However, current methods capture only one layer omics information at a time, precluding possibility examining mechanistic relationship across central dogma molecular biology. Here, we present two technologies spatially resolved, genome-wide, joint epigenome transcriptome by cosequencing chromatin accessibility gene expression, or histone modifications (H3K27me3, H3K27ac H3K4me3) expression on same section near-single-cell resolution. These were applied to embryonic juvenile mouse brain, as well adult human map how epigenetic mechanisms control transcriptional phenotype cell dynamics tissue. Although highly concordant features identified either also observed distinct patterns, suggesting their differential roles defining states. Linking pixel allows uncovering new insights priming, differentiation regulation within architecture. great interest life science biomedical research.

Language: Английский