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

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

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 …

Statistical and machine learning methods for spatially resolved transcriptomics data analysis

Z Zeng, Y Li, Y Li, Y Luo - Genome biology, 2022 - Springer
The recent advancement in spatial transcriptomics technology has enabled multiplexed
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …

TGF-β orchestrates fibrogenic and developmental EMTs via the RAS effector RREB1

J Su, SM Morgani, CJ David, Q Wang, EE Er… - Nature, 2020 - nature.com
Epithelial-to-mesenchymal transitions (EMTs) are phenotypic plasticity processes that confer
migratory and invasive properties to epithelial cells during development, wound-healing …

Multi-omics profiling of mouse gastrulation at single-cell resolution

R Argelaguet, SJ Clark, H Mohammed, LC Stapel… - Nature, 2019 - nature.com
Formation of the three primary germ layers during gastrulation is an essential step in the
establishment of the vertebrate body plan and is associated with major transcriptional …

Spatiotemporal omics for biology and medicine

L Liu, A Chen, Y Li, J Mulder, H Heyn, X Xu - Cell, 2024 - cell.com
The completion of the Human Genome Project has provided a foundational blueprint for
understanding human life. Nonetheless, understanding the intricate mechanisms through …

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

T Lohoff, S Ghazanfar, A Missarova, N Koulena… - Nature …, 2022 - nature.com
Molecular profiling of single cells has advanced our knowledge of the molecular basis of
development. However, current approaches mostly rely on dissociating cells from tissues …

[HTML][HTML] Capture of mouse and human stem cells with features of formative pluripotency

M Kinoshita, M Barber, W Mansfield, Y Cui, D Spindlow… - Cell stem cell, 2021 - cell.com
Pluripotent cells emerge as a naive founder population in the blastocyst, acquire capacity for
germline and soma formation, and then undergo lineage priming. Mouse embryonic stem …

[HTML][HTML] Uncovering an organ's molecular architecture at single-cell resolution by spatially resolved transcriptomics

J Liao, X Lu, X Shao, L Zhu, X Fan - Trends in biotechnology, 2021 - cell.com
Revealing fine-scale cellular heterogeneity among spatial context and the functional and
structural foundations of tissue architecture is fundamental within biological research and …

[HTML][HTML] Cell fate decisions, transcription factors and signaling during early retinal development

R Diacou, P Nandigrami, A Fiser, W Liu… - Progress in retinal and …, 2022 - Elsevier
The development of the vertebrate eyes is a complex process starting from anterior-posterior
and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye …