Open-ST: High-resolution spatial transcriptomics in 3D

Spatial transcriptomics (ST) methods unlock molecular mechanisms underlying tissue development, homeostasis, or disease. However, there is a need for easy-to-use, high-resolution, cost-efficient, and 3D-scalable methods. Here, we report Open-ST, a sequencing-based, open-source experimental and computational resource to address these challenges and to study the molecular organization of tissues in 2D and 3D. In mouse brain, Open-ST captured transcripts at subcellular resolution and reconstructed cell types. In primary head-and-neck tumors and patient-matched healthy/metastatic lymph nodes, Open-ST captured the diversity of immune, stromal, and tumor populations in space, validated by imaging-based ST. Distinct…

• JH
  Joachim Herz Stiftung
• DZ
  Deutsches Zentrum für Herz-Kreislaufforschung

  Award: 81X2100155
• EC
  European Commission

  Award: CN_00000041
• DA
  Deutscher Akademischer Austauschdienst
• DF
  Deutsche Forschungsgemeinschaft

  Awards: RA 838/5-1, KA 5006/1-1
• SU
  Syddansk Universitet
• BI
  Berlin Institute of Health
• L
  Leibniz-Gemeinschaft