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Updated: May 29, 2026
Fluorescence Activated Cell Sorting (FACS) and Gene Expression Analysis of Fos-expressing Neurons from Fresh and Frozen Rat Brain Tissue
Published on: August 27, 2016
Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples
Maggie L Chow1, Hai-Ri Li, Mary E Winn
1Department of Neuroscience, NIH-UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, 8110 La Jolla Shores Dr Ste 201, La Jolla, CA 92093, USA.
The cDNA-mediated annealing, selection, and ligation (DASL) assay offers more reliable gene expression profiling from degraded brain RNA than in vitro transcription (IVT) methods. This finding is crucial for studying brain tissue in neuropsychiatric disorders.
Area of Science:
- Molecular Biology
- Neuroscience
- Genomics
Background:
- Gene expression assays can provide high-quality data from degraded RNA.
- Application to postmortem human brain tissue is limited due to RNA quality challenges.
- Novel methods are needed to overcome technical limitations in brain tissue analysis.
Purpose of the Study:
- To compare the reliability of cDNA-mediated annealing, selection, and ligation (DASL) and in vitro transcription (IVT) assays.
- To evaluate these assays on RNA from various sources: artificially degraded pools, frozen brain tissue, and formalin-fixed brain tissue.
- To determine the suitability of DASL and IVT for genome-wide expression profiling in postmortem brain samples.
Main Methods:
- Comparison of DASL-based and IVT-based genome-wide expression profiling.
- Utilized RNA samples from artificially degraded reference pools.
- Tested RNA extracted from frozen human brain tissue and formalin-fixed human brain tissue.
Main Results:
- The DASL-based platform demonstrated superior reliability compared to the IVT-based platform for degraded reference brain RNA and frozen tissue samples.
- While both assays yielded poor results for a small set of formalin-fixed RNA samples, DASL showed greater reliability in specific probes and samples.
- DASL assays provided more dependable genome-wide expression data from challenging brain RNA samples.
Conclusions:
- The DASL-based gene expression profiling platform presents advantages for mRNA analysis in brain tissue over traditional IVT-based methods.
- These findings suggest DASL may be a more effective approach for gene expression studies in postmortem brain.
- The results have implications for research into neuropsychiatric disorders, potentially improving the analysis of affected brain tissues.
