ArticlePloS one2011
A quantitative comparison of cell-type-specific microarray gene expression profiling methods in the mouse brain.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 1 of them a synthesis that pooled it.
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Who cites it
68 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Modeling sources of interlaboratory variability in electrophysiological properties of mammalian neurons.Journal of neurophysiology · 2018Pooled it
- Comparative Analysis of Plasma Extracellular Vesicle Isolation Methods for Purity Assessment and Biomarker Discovery.Proteomes · 2025Article
- Matrix Inversion and Subset Selection (MISS): A pipeline for mapping of diverse cell types across the murine brain.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Microglial identity and inflammatory responses are controlled by the combined effects of neurons and astrocytes.Cell reports · 2021Article
- Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.Frontiers in molecular neuroscience · 2021Article
- The Therapeutic Potential of Mesenchymal Stem Cell-Derived Exosomes in Treatment of Neurodegenerative Diseases.Molecular neurobiology · 2019Review
- Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons.Scientific reports · 2019Article
- Article
- Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription.Nature protocols · 2018Article
- The Future of Cross-Linking and Immunoprecipitation (CLIP).Cold Spring Harbor perspectives in biology · 2018Review
- Assessing Transcriptome Quality in Patch-Seq Datasets.Frontiers in molecular neuroscience · 2018Article
- Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees.Advances in neurobiology · 2018Article
- The Expanding Toolkit of Translating Ribosome Affinity Purification.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2017Article
- Transcriptomic correlates of neuron electrophysiological diversity.PLoS computational biology · 2017Article
- Article
- Article
- Identification of preoptic sleep neurons using retrograde labelling and gene profiling.Nature · 2017Article
- Astrocytes locally translate transcripts in their peripheral processes.Proceedings of the National Academy of Sciences of the United States of America · 2017Review
- Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism.Nature communications · 2017Article
- A Comprehensive Analysis of Cell Type-Specific Nuclear RNA From Neurons and Glia of the Brain.Biological psychiatry · 2017Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Expression profiling of restricted neural populations using microarrays can facilitate neuronal classification and provide insight into the molecular bases of cellular phenotypes. Due to the formidable heterogeneity of intermixed cell types that make up the brain, isolating cell types prior to microarray processing poses steep technical challenges that have been met in various ways. These methodological differences have the potential to distort cell-type-specific gene expression profiles insofar as they may insufficiently filter out contaminating mRNAs or induce aberrant cellular responses not normally present in vivo. Thus we have compared the repeatability, susceptibility to contamination from off-target cell-types, and evidence for stress-responsive gene expression of five different purification methods--Laser Capture Microdissection (LCM), Translating Ribosome Affinity Purification (TRAP), Immunopanning (PAN), Fluorescence Activated Cell Sorting (FACS), and manual sorting of fluorescently labeled cells (Manual). We found that all methods obtained comparably high levels of repeatability, however, data from LCM and TRAP showed significantly higher levels of contamination than the other methods. While PAN samples showed higher activation of apoptosis-related, stress-related and immediate early genes, samples from FACS and Manual studies, which also require dissociated cells, did not. Given that TRAP targets actively translated mRNAs, whereas other methods target all transcribed mRNAs, observed differences may also reflect translational regulation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.