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Related Experiment Video

Updated: Aug 28, 2025

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Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling.

Stephanie M Zimmerman1, Robin Fropf1, Bridget R Kulasekara1

  • 1NanoString Technologies, Seattle, Washington 98109, USA.

Genome Research
|September 13, 2022
PubMed
Summary
This summary is machine-generated.

New spatial profiling technology quantifies whole transcriptomes in human and mouse tissues. This Whole Transcriptome Atlas (WTA) enables detailed spatial gene expression analysis across diverse biological samples.

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Area of Science:

  • Genomics and Molecular Biology
  • Spatial Transcriptomics
  • Bioinformatics

Background:

  • High-plex molecular profiling in tissues preserves spatial and morphological context of gene expression.
  • Digital Spatial Profiling (DSP) platforms offer advanced capabilities for tissue analysis.

Purpose of the Study:

  • To expand the chemistry for the Digital Spatial Profiling platform for whole transcriptome quantification.
  • To develop and validate the human and mouse Whole Transcriptome Atlas (WTA) for spatial profiling.
  • To assess WTA performance across diverse tissue types and biological contexts.

Main Methods:

  • Design of multiplexed in situ hybridization probes for human and mouse protein-coding genes.
  • Validation of WTA in cell lines against orthogonal gene expression profiling methods.
  • Benchmarking transcript detection sensitivity against bulk RNA-seq and fluorescence in situ hybridization.

Main Results:

  • Robust transcript detection down to approximately 100 transcripts per region was achieved.
  • WTA successfully identified gene expression differences between tumor and tumor microenvironment.
  • Spatial profiling revealed disease-specific gene expression heterogeneity in kidney structures and mapped transcriptional programs in developing mouse embryos.

Conclusions:

  • The Whole Transcriptome Atlas (WTA) assays provide a flexible method for spatial whole transcriptome profiling.
  • Digital Spatial Profiling technology with WTA is applicable to diverse tissue types and biological questions.
  • This approach advances the understanding of spatial gene expression in cancer, pathology, and developmental biology.