Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues

    September 2024
    Soichiro Asami, C. C. Yin, Luis A. Garza, Reza Kalhor
    TLDR 3DEEP reveals early hair follicle stem cell formation and niche establishment before hair bulb development.
    The study introduces 3DEEP, a novel tissue clearing and spatial transcriptomic method, to analyze organ development in thick tissues, specifically focusing on hair follicles. Researchers examined 371 hair follicles in a 1 mm³ skin sample from a 12-hour-old mouse, capturing 6 million transcripts from 81 genes. This approach allowed them to create a 3D atlas of hair follicle development, identifying molecular stages and structural changes during organogenesis. Key findings include the early establishment of hair follicle stem cells and their niche before hair bulb formation. The study highlights the potential of spatial transcriptomics for detailed, four-dimensional analysis of organ development.
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