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<p>Imaging-based spatial transcriptomics methods allow for the measurement of spatial determinants of cellular phenotypes but are incompatible with random barcode-based clone-tracing methods, preventing the simultaneous detection of clonal and spatial drivers. Here we report SpaceBar, which enables simultaneous clone tracing and spatial gene expression profiling with standard imaging-based spatial transcriptomics pipelines. Our approach uses a library of 96 synthetic barcode sequences that combinatorially labels each cell. Thus, SpaceBar can distinguish between clonal dynamics and environmentally driven transcriptional regulation in complex tissue contexts.</p>

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SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics

  • 期刊论文

  • 发表日期：

    2025年12月18日

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  • Grant Kinsler,
  • Caitlin Fagan,
  • Haiyin Li,
  • Jessica Kaster,
  • Maggie Dunne,
  • Robert J. Vander Velde,
  • Ryan H. Boe,
  • Sydney Shaffer,
  • Meenhard Herlyn,
  • Arjun Raj,
  • Yael Heyman

摘要

Imaging-based spatial transcriptomics methods allow for the measurement of spatial determinants of cellular phenotypes but are incompatible with random barcode-based clone-tracing methods, preventing the simultaneous detection of clonal and spatial drivers. Here we report SpaceBar, which enables simultaneous clone tracing and spatial gene expression profiling with standard imaging-based spatial transcriptomics pipelines. Our approach uses a library of 96 synthetic barcode sequences that combinatorially labels each cell. Thus, SpaceBar can distinguish between clonal dynamics and environmentally driven transcriptional regulation in complex tissue contexts.