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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Jun 26, 2025

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

Published on: April 30, 2019

ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs.

Xinyu Hu^1,2, Bob van Sluijs¹, Óscar García-Blay^1,2

¹Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.

Nature Communications

|May 9, 2024

Summary

Cellular position on micropatterns influences gene expression. New ARTseq-FISH method reveals early mRNA and protein changes, impacting cell fate decisions during stem cell differentiation.

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Last Updated: Jun 26, 2025

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

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Published on: April 30, 2019

Author Spotlight: Investigating mRNA Spatial Distribution in Drosophila Muscle Tissue

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Stem cell biology
Developmental biology
Molecular cell biology

Background:

Cell fate decisions are influenced by heterogeneous gene expression.
The impact of micropattern localization on early gene expression changes (mRNA, protein, phosphoprotein) is not well understood.

Purpose of the Study:

To investigate how cellular position on a micropattern affects gene expression.
To develop a method for simultaneous profiling of mRNA, protein, and phosphoprotein in single cells.

Main Methods:

Developed a scalable antibody and mRNA targeting sequential fluorescence in situ hybridization (ARTseq-FISH) method.
Studied 67 (phospho-)protein and mRNA targets in mouse embryonic stem cells (mESCs) on circular micropatterns.
Utilized conventional immunofluorescence and time-lapse microscopy for confirmation.

Main Results:

ARTseq-FISH revealed changes in mRNA and (phospho-)protein abundance and localization within 48 hours of exiting pluripotency.
Cells near the micropattern edge showed increased proliferation compared to central cells.
Position-dependent differences in mRNA and protein levels emerged as early as 12 hours after LIF withdrawal.

Conclusions:

Micropattern localization induces position-dependent gene expression changes in early stem cell differentiation.
ARTseq-FISH is a powerful tool for studying single-cell heterogeneity in gene expression.
Early emergence of spatial gene expression differences suggests a role in cell fate decisions.