ArticleBio-protocol2023
Quantitative Analysis of Gene Expression in RNAscope-processed Brain Tissue.
Article in Bio-protocol, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Distribution of Metabotropic Serotonin Receptors in GABAergic and Glutamatergic Neurons in the Auditory Midbrain.The Journal of comparative neurology · 2026Article
- Sexually dimorphic effects of single prolonged stress on conditioned suppression behavior in Long Evans rats with no detection of altered mRNA expression of VGLUT1, GAD1, and Arc in the ventral hippocampus.Frontiers in behavioral neuroscience · 2026Article
- Peroxisomes and the nervous system: progress and challenges in neuroinflammation and cell-specific functions.Frontiers in molecular neuroscience · 2026Article
- Suppression of NRAS-mutant melanoma growth with NRAS-targeting Antisense Oligonucleotide treatment reveals therapeutically relevant kinase co-dependencies.Communications medicine · 2025Article
- Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum.bioRxiv : the preprint server for biology · 2025Article
- Septo-hypothalamic regulation of binge-like alcohol consumption by the nociceptin system.Cell reports · 2025Article
- Accessing genetically defined cell types in the superior colliculus with transgenic mouse lines.iScience · 2025Article
- Endothelial cell-specific postnatal deletion of Nos3 preserves intraocular pressure homeostasis via macrophage recruitment and NOS2 upregulation.The Journal of clinical investigation · 2025Article
- Spatial differences in gene expression across the dorsal raphe nucleus in a model of early Alzheimer's disease.Journal of Alzheimer's disease : JAD · 2025Article
- Chronic alcohol withdrawal-associated increases in VTAAdvances in drug and alcohol research · 2025Article
- Astrocyte tau deposition in progressive supranuclear palsy is associated with dysregulation of MAPT transcription.Acta neuropathologica communications · 2024Article
- Interaction of serotonin/GLP-1 circuitry in a dual preclinical model for psychiatric disorders and metabolic dysfunction.Psychiatry research · 2024Article
- A comparison of confocal and epifluorescence microscopy for quantification of RNAScope and immunohistochemistry fluorescent images.Journal of neuroscience methods · 2024Article
- Long-lasting mechanical hypersensitivity and CRF receptor type-1 neuron activation in the BNST following adolescent ethanol exposure.Alcohol, clinical & experimental research · 2024Article
- High dose administration of DREADD agonist JHU37160 produces increases in anxiety-like behavior in male rats.Behavioural brain research · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Molecular characterization of different cell types in rodent brains is a widely used and important approach in neuroscience. Fluorescent detection of transcripts using RNAscope (ACDBio) has quickly became a standard in situ hybridization (ISH) approach. Its sensitivity and specificity allow for the simultaneous detection of between three and forty-eight low abundance mRNAs in single cells (i.e., multiplexing or hiplexing), and, in contrast to other ISH techniques, it is performed in a shorter amount of time. Manual quantification of transcripts is a laborious and time-consuming task even for small portions of a larger tissue section. Herein, we present a protocol for creating high-quality images for quantification of RNAscope-labeled neurons in the rat brain. This protocol uses custom-made scripts within the open-source software QuPath to create an automated workflow for the careful optimization and validation of cell detection parameters. Moreover, we describe a method to derive mRNA signal thresholds using negative controls. This protocol and automated workflow may help scientists to reliably and reproducibly prepare and analyze rodent brain tissue for cell type characterization using RNAscope. Graphical abstract.
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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.