ArticleFrontiers in cellular neuroscience2018
A Guide to Single-Cell Transcriptomics in Adult Rodent Brain: The Medium Spiny Neuron Transcriptome Revisited.
Article in Frontiers in cellular neuroscience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
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- Deficiency of Cullin 3, a Protein Encoded by a Schizophrenia and Autism Risk Gene, Impairs Behaviors by Enhancing the Excitability of Ventral Tegmental Area (VTA) DA Neurons.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2023Article
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- Identification of visual cortex cell types and species differences using single-cell RNA sequencing.Nature communications · 2022Article
- Gossypetin ameliorates 5xFAD spatial learning and memory through enhanced phagocytosis against Aβ.Alzheimer's research & therapy · 2022Article
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- Translational profiling of mouse dopaminoceptive neurons reveals region-specific gene expression, exon usage, and striatal prostaglandin E2 modulatory effects.Molecular psychiatry · 2022Article
- Shisa6 mediates cell-type specific regulation of depression in the nucleus accumbens.Molecular psychiatry · 2021Article
- Combined Mechanical and Enzymatic Dissociation of Mouse Brain Hippocampal Tissue.Journal of visualized experiments : JoVE · 2021Article
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- Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda.Neuroinformatics · 2021Article
- Facilitating mGluR4 activity reverses the long-term deleterious consequences of chronic morphine exposure in male mice.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2021Article
- Two alternative methods for the retrieval of somatic cell populations from the mouse ovary.Molecular human reproduction · 2021Article
- Expression of FoxP2 in the basal ganglia regulates vocal motor sequences in the adult songbird.Nature communications · 2021Article
- Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks.Nature communications · 2021Article
- Gene Families With Stochastic Exclusive Gene Choice Underlie Cell Adhesion in Mammalian Cells.Frontiers in cell and developmental biology · 2021Article
- Open Frontiers in Neural Cell Type Investigations; Lessons FromFrontiers in neuroscience · 2021Review
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15 authors.
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Abstract
Recent advances in single-cell technologies are paving the way to a comprehensive understanding of the cellular complexity in the brain. Protocols for single-cell transcriptomics combine a variety of sophisticated methods for the purpose of isolating the heavily interconnected and heterogeneous neuronal cell types in a relatively intact and healthy state. The emphasis of single-cell transcriptome studies has thus far been on comparing library generation and sequencing techniques that enable measurement of the minute amounts of starting material from a single cell. However, in order for data to be comparable, standardized cell isolation techniques are essential. Here, we analyzed and simplified methods for the different steps critically involved in single-cell isolation from brain. These include enzymatic digestion, tissue trituration, improved methods for efficient fluorescence-activated cell sorting in samples containing high degree of debris from the neuropil, and finally, highly region-specific cellular labeling compatible with use of stereotaxic coordinates. The methods are exemplified using medium spiny neurons (MSN) from dorsomedial striatum, a cell type that is clinically relevant for disorders of the basal ganglia, including psychiatric and neurodegenerative diseases. We present single-cell RNA sequencing (scRNA-Seq) data from D1 and D2 dopamine receptor expressing MSN subtypes. We illustrate the need for single-cell resolution by comparing to available population-based gene expression data of striatal MSN subtypes. Our findings contribute toward standardizing important steps of single-cell isolation from adult brain tissue to increase comparability of data. Furthermore, our data redefine the transcriptome of MSNs at unprecedented resolution by confirming established marker genes, resolving inconsistencies from previous gene expression studies, and identifying novel subtype-specific marker genes in this important cell type.
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