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Spatial Transcriptomics

All articles tagged with #spatial transcriptomics

Skin’s cellular map reveals TNF-driven immune–fibroblast networks in SALT-like neighborhoods
science19 days ago

Skin’s cellular map reveals TNF-driven immune–fibroblast networks in SALT-like neighborhoods

Researchers generated an organ-wide, MERFISH-based single-cell spatial atlas of about 1.2 million cells from normal adult human skin, spanning 15 body sites and 22 donors, resolving 45 cell types and 10 multicellular neighborhoods. They highlight a perivascular neighborhood reminiscent of skin-associated lymphoid tissue (SALT) where TNF coordinates immune–fibroblast crosstalk, with CCL19+ fibroblasts proximal to vessels playing a central role. By integrating MERFISH with scRNA-seq and Visium data, they map site-specific cellular compositions, neighborhood dynamics, and ligand–receptor signaling, and show pan-disease immune alterations in the perivascular niche across skin conditions. An interactive web tool is provided to explore these data, underscoring spatial organization as a key driver of skin biology and disease.

via Nature|
#salt#science#single-cell-atlas
Developmental cell states drive heterogeneity in supratentorial ependymomas
science1 month ago

Developmental cell states drive heterogeneity in supratentorial ependymomas

A multidimensional study integrating single-cell and spatial transcriptomics with live-cell imaging reveals two progenitor-like states—neuroepithelial-like and embryonic-like—and diverse spatial architectures in supratentorial ependymomas. Brain-resident cells can shift tumor cells toward neuronal-like, migratory phenotypes, highlighting developmental origins of heterogeneity and suggesting potential therapeutic angles.

via Nature|
#ependymoma#science#single-cell-rna-seq
Mapping the Developing Human Heart to Understand Congenital Defects
science5 months ago

Mapping the Developing Human Heart to Understand Congenital Defects

This study provides a detailed spatiotemporal map of gene expression and cellular dynamics during early human heart development, analyzing over 69,000 tissue spots and nearly 77,000 cells across 36 hearts, revealing diverse cell types, specialized conduction system components, and the formation of cardiac innervation and valves, thereby advancing understanding of human cardiogenesis.

via Nature|
#cardiogenesis#cellular-dynamics#human-heart-development
Unveiling the Intricate Development of Human Limbs: From Embryonic Atlas to Nature's Chiseling
science-and-technology2 years ago

Unveiling the Intricate Development of Human Limbs: From Embryonic Atlas to Nature's Chiseling

Researchers have created a comprehensive atlas of human embryonic limb development using single-cell transcriptomic RNA sequencing and spatial transcriptomic sequencing. The study identified 67 distinct cell clusters and mapped their spatial distribution across four timepoints during the first trimester of development. The research sheds light on the cellular heterogeneity, patterning events, and gene expression patterns associated with limb malformations. The findings also highlight the similarities between human limb development and that of model organisms like mice. This atlas provides valuable insights into the complex processes involved in limb development and can serve as a reference for studying genetic variations and developmental disorders.

via Nature.com|
#gene-expression-patterns#human-embryonic-limb-development#limb-malformations
Unraveling the Inflammatory Puzzle: How Obesity and Immune Cells Interact in Fat Tissue
health2 years ago

Unraveling the Inflammatory Puzzle: How Obesity and Immune Cells Interact in Fat Tissue

A study conducted by researchers at the University of Michigan has revealed new insights into the complex inflammatory response that occurs within fat tissue in obesity. Using single cell analysis and spatial transcriptomics, the study identified previously unrecognized immune cell types and interactions within adipose tissue. The researchers discovered different subtypes of macrophages, with some exhibiting pro-inflammatory genes and others showing low pro-inflammatory gene expression. The findings suggest that the body may attempt to counter inflammation by promoting lipid-associated macrophages. Further research will focus on understanding the signaling processes and proteins associated with the development of these macrophages and metabolic disorders.

via Medical Xpress|
#fat-tissue#health#immune-cells
"Unraveling the Mysteries: Mapping the Intricate Mouse Brain"
neuroscience2 years ago

"Unraveling the Mysteries: Mapping the Intricate Mouse Brain"

Researchers are making significant progress in mapping the mouse brain by combining high-throughput single-cell RNA sequencing with spatial transcriptomics. These methods allow for the identification and mapping of different categories of brain cells, providing comprehensive atlases of the mouse brain. The next steps involve understanding the functions of these molecularly defined cell types and creating a unified resource for the neuroscience community. These efforts are part of the larger BRAIN Initiative Cell Census Network, which aims to create comprehensive maps of cells in the brains of mice and primates, including humans.

via Nature.com|
#brain-mapping#cellular-diversity#mouse-brain
Revolutionary Tool Enhances Neuron Sequencing Capabilities
neuroscience2 years ago

Revolutionary Tool Enhances Neuron Sequencing Capabilities

Researchers at Stanford have developed a new technique called expansion spatial transcriptomics (Ex-ST) that significantly improves the resolution of spatial transcriptomics, a method used to identify and classify different types of brain cells based on gene expression patterns. By expanding brain tissue, the researchers were able to capture mRNA from individual cells with greater precision, allowing for a more detailed understanding of neuron types and their functions. The Ex-ST method is expected to have a significant impact on neuroscience research and may pave the way for further advancements in studying the structure and function of brain tissue.

via Medical Xpress|
#brain-tissue-expansion#gene-expression-profiling#neuro-omics-initiative
The Value of User-Friendly Computational Methods
science-and-technology3 years ago

The Value of User-Friendly Computational Methods

Making computational methods accessible to others is crucial for scientific progress. Jean Fan, an assistant professor at Johns Hopkins University, developed a method called STdeconvolve to analyze spatial transcriptomics data. She made the code available on GitHub and simplified installation through Bioconductor. She also shared a video of herself live-coding a spatial transcriptomics data analysis on YouTube and shared blog posts and tutorials to support students. By increasing accessibility, STdeconvolve is easier to maintain and use, and students can provide feedback and build communities.

via Nature.com|
#accessibility#computational-methods#open-source