Embryo-scale, single-cell spatial transcriptomics

SR Srivatsan, MC Regier, E Barkan, JM Franks… - Science, 2021 - science.org
Spatial patterns of gene expression manifest at scales ranging from local (eg, cell-cell
interactions) to global (eg, body axis patterning). However, current spatial transcriptomics …

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

A Chen, S Liao, M Cheng, K Ma, L Wu, Y Lai, X Qiu… - Cell, 2022 - cell.com
Spatially resolved transcriptomic technologies are promising tools to study complex
biological processes such as mammalian embryogenesis. However, the imbalance between …

Spatially resolved epigenomic profiling of single cells in complex tissues

T Lu, CE Ang, X Zhuang - Cell, 2022 - cell.com
The recent development of spatial omics methods has enabled single-cell profiling of the
transcriptome and 3D genome organization with high spatial resolution. Expanding the …

Museum of spatial transcriptomics

L Moses, L Pachter - Nature methods, 2022 - nature.com
The function of many biological systems, such as embryos, liver lobules, intestinal villi, and
tumors, depends on the spatial organization of their cells. In the past decade, high …

Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope

X Wan, J Xiao, SST Tam, M Cai, R Sugimura… - Nature …, 2023 - nature.com
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our
understanding of tissue spatial architecture and biology. Although current ST methods …

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

E Lein, LE Borm, S Linnarsson - Science, 2017 - science.org
The stereotyped spatial architecture of the brain is both beautiful and fundamentally related
to its function, extending from gross morphology to individual neuron types, where soma …

Mapping cells through time and space with moscot

D Klein, G Palla, M Lange, M Klein, Z Piran, M Gander… - bioRxiv, 2023 - biorxiv.org
Single-cell genomics technologies enable multimodal profiling of millions of cells across
temporal and spatial dimensions. Experimental limitations prevent the measurement of all …

Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view

J Zhu, K Pang, B Hu, R He, N Wang, Z Jiang, P Ji… - Nature Genetics, 2024 - nature.com
Spatial transcriptomic techniques offer unprecedented insights into the molecular
organization of complex tissues. However, integrating cost-effectiveness, high throughput, a …

A high-resolution anatomical atlas of the transcriptome in the mouse embryo

G Diez-Roux, S Banfi, M Sultan, L Geffers, S Anand… - PLoS …, 2011 - journals.plos.org
Ascertaining when and where genes are expressed is of crucial importance to
understanding or predicting the physiological role of genes and proteins and how they …

Advances and challenges in spatial transcriptomics for developmental biology

K Choe, U Pak, Y Pang, W Hao, X Yang - Biomolecules, 2023 - mdpi.com
Development from single cells to multicellular tissues and organs involves more than just the
exact replication of cells, which is known as differentiation. The primary focus of research …