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Related Experiment Video

Updated: Jan 18, 2026

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

Published on: October 25, 2018

Protocol for single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding

Haylie R Helms¹, Luiz E Bertassoni²

¹Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97201, USA; Knight Cancer Precision Biofabrication Hub, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA.

|September 12, 2025

Summary

We developed a new protocol for spatial transcriptomic analysis of 2D engineered tissues and cell cultures. This method is compatible with Visium HD spatial technology, enabling detailed cellular insights.

Keywords:

Biotechnology and bioengineering Cancer Cell Biology Cell culture Cell-based Assays Gene Expression Genomics Microscopy Sequence analysis Sequencing Single Cell Tissue Engineering

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Last Updated: Jan 18, 2026

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

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Published on: October 25, 2018

Transcriptome Analysis of Single Cells

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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Area of Science:

Biotechnology
Molecular Biology
Genomics

Background:

Spatial transcriptomics reveals cellular composition and spatial relationships influencing cell behavior.
Standard protocols often require embedding and sectioning, limiting analysis of 2D engineered tissues and cell cultures.

Purpose of the Study:

To present a novel protocol for spatial transcriptomic profiling of 2D engineered tissues and cell cultures.
To adapt existing methods for compatibility with Visium HD spatial technology.

Main Methods:

Detailed steps for sample generation, fixation, and staining are provided.
The protocol is designed for 2D engineered tissues and cell cultures incompatible with standard embedding and sectioning.
Integration with Visium HD spatial technology is a key feature.

Main Results:

A flexible and effective protocol for spatial transcriptomic analysis of challenging 2D samples.
Successful adaptation of spatial transcriptomics for engineered tissues and cell cultures.
Enables detailed investigation of cellular microenvironments.

Conclusions:

This protocol expands the application of spatial transcriptomics to a wider range of biological systems.
It offers a valuable tool for researchers studying cellular interactions in 2D cultures and engineered tissues.
Facilitates deeper understanding of spatial gene expression patterns.