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Related Experiment Video

Updated: Feb 26, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
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Volumetric DNA microscopy for mapping spatial transcriptomes in three dimensions.

Nianchao Qian1, Jing Li1, Reem Yasser2

  • 1Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA.

Nature Protocols
|February 24, 2026
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Summary
This summary is machine-generated.

Volumetric DNA microscopy profiles spatial transcriptomes in intact tissues without optics. This scalable method reconstructs 3D cellular organization and microenvironments using DNA encoding and sequencing.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Biological systems are inherently 3D, but current spatial transcriptomics methods are limited to 2D tissue sections.
  • This limitation hinders the resolution of cellular organization and microenvironments within intact tissue volumes.

Purpose of the Study:

  • To develop a scalable, optics-free method for spatial transcriptome profiling directly within intact biological specimens.
  • To enable the reconstruction of three-dimensional spatial relationships for comprehensive tissue analysis.

Main Methods:

  • Developed volumetric DNA microscopy, encoding spatial information into DNA molecules within an intermolecular network.
  • Detailed workflow: in situ cDNA synthesis, DNA nanoball formation for spatial encoding, proximity bridging, and 3D reconstruction via geodesic spectral embedding.
  • Utilizes routine molecular biology reagents and a benchtop sequencer for library generation and computational analysis.

Main Results:

  • Successfully established a complete workflow for volumetric spatial transcriptome profiling in intact tissues.
  • Demonstrated the capability to reconstruct three-dimensional spatial relationships through DNA encoding and short-read sequencing.
  • Workflow is efficient, with sequencing libraries generated in 7-8 days.

Conclusions:

  • Volumetric DNA microscopy offers a versatile platform for exploring genetic and morphological features in intact tissues.
  • Overcomes limitations of 2D tissue sectioning, providing deeper insights into tissue architecture and cellular interactions.
  • Accessible technology for researchers using standard molecular biology techniques and equipment.