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Related Experiment Video

Updated: Jan 18, 2026

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

Published on: May 16, 2025

Fishing with Two Lines: A Hybrid Approach to Spatial Transcriptomic Discovery.

Arianna L Williams-Katek¹, Saahithi Mallapragada^1,2, Evan D Mee¹

¹Division of Bioinnovation and Genome Sciences, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States.

Biorxiv : the Preprint Server for Biology

|January 16, 2026

Summary

This summary is machine-generated.

This study introduces a dual chemistry spatial transcriptomics method, combining high-sensitivity and broad-coverage panels. This approach enhances cell retention and data richness for sensitive gene profiling and discovery.

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Last Updated: Jan 18, 2026

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

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Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

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Published on: September 20, 2020

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Spatial transcriptomics enables gene expression analysis within tissue context.
Current methods face a trade-off between the number of genes analyzed and per-gene sensitivity.
High-sensitivity panels assay fewer genes, while broad-coverage panels have lower sensitivity.

Purpose of the Study:

To develop a novel dual chemistry method for spatial transcriptomics.
To combine high sensitivity (Xenium V1 panel) and broad coverage (Prime 5K panel) on a single tissue section.
To overcome the limitations of existing spatial transcriptomics approaches.

Main Methods:

Developed a 'dual chemistry' approach by co-hybridizing Prime and Xenium V1 probes.
Sequentially performed V1 and Prime decoding chemistries on the same tissue section.
Validated the method on a human lung tissue microarray.

Main Results:

Achieved high concordance between independent V1 and Prime chemistry runs and the dual chemistry approach.
Observed similar expression patterns for overlapping genes in the dual run, confirming assay fidelity.
Demonstrated successful integration of high sensitivity and broad coverage profiling.

Conclusions:

The dual chemistry method effectively integrates high-sensitivity and broad-coverage spatial transcriptomics.
This approach enhances cell retention and provides richer biological information.
Enables both sensitive gene expression profiling and broader discovery in spatial transcriptomics studies.