The emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

[HTML][HTML] Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

M Cheng, Y Jiang, J Xu, AFA Mentis, S Wang… - Journal of Genetics and …, 2023 - Elsevier
The ability to explore life kingdoms is largely drive by innovations and breakthroughs in
technology, from the invention of the microscope 350 years ago to the recent emergence of …

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Z Liu, X Kong, Y Long, S Liu, H Zhang, J Jia, W Cui… - Nature Plants, 2023 - nature.com
Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing
nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell …

[HTML][HTML] An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte–tumor cell crosstalk, local immunosuppression and tumor progression

L Wu, J Yan, Y Bai, F Chen, X Zou, J Xu, A Huang… - Cell research, 2023 - nature.com
Dissecting and understanding the cancer ecosystem, especially that around the tumor
margins, which have strong implications for tumor cell infiltration and invasion, are essential …

Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum)

Y Qin, M Sun, W Li, M Xu, L Shao, Y Liu… - Plant biotechnology …, 2022 - Wiley Online Library
Cotton fibre is a unicellular seed trichome, and lint fibre initials per seed as a factor
determines fibre yield. However, the mechanisms controlling fibre initiation from ovule …

Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus

X Song, P Guo, K Xia, M Wang, Y Liu… - Proceedings of the …, 2023 - National Acad Sciences
Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation
in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot …

[HTML][HTML] Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap

T Nobori, M Oliva, R Lister, JR Ecker - Nature Plants, 2023 - nature.com
Retrieving the complex responses of individual cells in the native three-dimensional tissue
context is crucial for a complete understanding of tissue functions. Here, we present …

[PDF][PDF] Single-cell technologies: From research to application

L Wen, G Li, T Huang, W Geng, H Pei, J Yang, M Zhu… - The Innovation, 2022 - cell.com
In recent years, more and more single-cell technologies have been developed. A vast
amount of single-cell omics data has been generated by large projects, such as the Human …

[HTML][HTML] Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

S Saarenpää, O Shalev, H Ashkenazy, V Carlos… - Nature …, 2023 - nature.com
The interactions of microorganisms among themselves and with their multicellular host take
place at the microscale, forming complex networks and spatial patterns. Existing technology …

STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization

Z Xu, W Wang, T Yang, L Li, X Ma, J Chen… - Nucleic Acids …, 2024 - academic.oup.com
Recent technological developments in spatial transcriptomics allow researchers to measure
gene expression of cells and their spatial locations at the single-cell level, generating …