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Related Experiment Video

Updated: Jul 16, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

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

Published on: July 6, 2022

Mitigating Fixation Artifacts in Spatial Transcriptomics: Methodological Insights from Human Brain Tissue.

Kassandra Georges1,2, Maiken Krogsbaek3,4, Sara Newell Jensen5

  • 1Core Center for Molecular Morphology, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark. kasgeo@biomed.au.dk.

Molecular Neurobiology
|July 15, 2026
PubMed
Summary

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New methods allow transcriptome analysis in long-term formalin-fixed human brain tissue. This study optimized RNA retrieval and identified 932 differentially expressed genes in hypothalamic neurons and microglia.

Area of Science:

  • Neuroscience
  • Genomics
  • Biotechnology

Background:

  • Human brain banks are valuable for disease research but limited by RNA quality in fixed tissues.
  • Long-term formalin fixation historically hinders transcriptomic studies.
  • Emerging sensitive techniques enable human transcriptome analysis in autopsied brain samples.

Purpose of the Study:

  • Develop a protocol for RNA expression analysis in distinct cell populations from fixed human hypothalamus.
  • Utilize the GeoMx Digital Spatial Profiler for spatial transcriptomics.
  • Optimize RNA retrieval and binding conditions for aged formalin-fixed samples.

Main Methods:

  • Optimized RNA retrieval using RNAscope assays and QuPath quantification.
  • Applied heat-induced target retrieval (60°C for 1h, then 99°C for 30min) while preserving tissue integrity.
Keywords:
Brain bankFixed tissueRNAscopeSpatial transcriptomicsTarget retrieval

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Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience
08:14

Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience

Published on: August 26, 2014

Related Experiment Videos

Last Updated: Jul 16, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

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

Published on: July 6, 2022

Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience
08:14

Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience

Published on: August 26, 2014

  • Used GeoMx Digital Spatial Profiler for whole transcriptome analysis of microglia (Iba1) and neurons (CRH) segments.
  • Employed the StandR bioinformatic tool for data analysis.

    • Main Results:

    • Identified 932 differentially expressed genes between neuronal and microglial segments.
    • Found 317 genes upregulated in the CRH (neuronal) segment.
    • Detected 615 genes upregulated in the Iba1 (microglial) segment.

    Conclusions:

    • Presents a detailed workflow for spatial transcriptomics on long-term fixed human brain tissue.
    • Demonstrates the feasibility of obtaining relevant transcriptomic data from challenging samples.
    • Highlights the potential for studying disease mechanisms in archival brain specimens.