Faculty Opinions recommendation of An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.

2014 ◽  
Author(s):  
Q Richard Lu
Keyword(s):  
Cerebral Cortex ◽  
Rna Sequencing ◽  
Vascular Cells

scholarly journals An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

2014 ◽  
Vol 34 (36) ◽  
pp. 11929-11947 ◽  
Author(s):  
Y. Zhang ◽  
K. Chen ◽  
S. A. Sloan ◽  
M. L. Bennett ◽  
A. R. Scholze ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
Rna Sequencing ◽  
Vascular Cells

scholarly journals Transcriptomic Modification in the Cerebral Cortex following Noninvasive Brain Stimulation: RNA-Sequencing Approach

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
Ben Holmes ◽  
Seung Ho Jung ◽  
Jing Lu ◽  
Jessica A. Wagner ◽  
Liudmilla Rubbi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Current Intensity ◽  
Beneficial Effects ◽  
Group A ◽  
The Impact

Transcranial direct current stimulation (tDCS) has been shown to modulate neuroplasticity. Beneficial effects are observed in patients with psychiatric disorders and enhancement of brain performance in healthy individuals has been observed following tDCS. However, few studies have attempted to elucidate the underlying molecular mechanisms of tDCS in the brain. This study was conducted to assess the impact of tDCS on gene expression within the rat cerebral cortex. Anodal tDCS was applied at 3 different intensities followed by RNA-sequencing and analysis. In each current intensity, approximately 1,000 genes demonstrated statistically significant differences compared to the sham group. A variety of functional pathways, biological processes, and molecular categories were found to be modified by tDCS. The impact of tDCS on gene expression was dependent on current intensity. Results show that inflammatory pathways, antidepressant-related pathways (GTP signaling, calcium ion binding, and transmembrane/signal peptide pathways), and receptor signaling pathways (serotonergic, adrenergic, GABAergic, dopaminergic, and glutamate) were most affected. Of the gene expression profiles induced by tDCS, some changes were observed across multiple current intensities while other changes were unique to a single stimulation intensity. This study demonstrates that tDCS can modify the expression profile of various genes in the cerebral cortex and that these tDCS-induced alterations are dependent on the current intensity applied.

scholarly journals Single-cell RNA sequencing reveals the cellular heterogeneity of aneurysmal infrarenal abdominal aorta

2020 ◽  
Author(s):  
Guizhen Zhao ◽  
Haocheng Lu ◽  
Ziyi Chang ◽  
Yang Zhao ◽  
Tianqing Zhu ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Single Cell ◽  
Rna Sequencing ◽  
Clustering Analysis ◽  
Cellular Response ◽  
Cellular Responses ◽  
Cellular Heterogeneity ◽  
Vascular Cells ◽  
Transcriptional Profiles ◽  
Single Cell Rna Sequencing

Abstract Aims The artery contains numerous cell types which contribute to multiple vascular diseases. However, the heterogeneity and cellular responses of these vascular cells during abdominal aortic aneurysm (AAA) progression have not been well characterized. Methods and results Single-cell RNA sequencing was performed on the infrarenal abdominal aortas (IAAs) from C57BL/6J mice at Days 7 and 14 post-sham or peri-adventitial elastase-induced AAA. Unbiased clustering analysis of the transcriptional profiles from >4500 aortic cells identified 17 clusters representing nine-cell lineages, encompassing vascular smooth muscle cells (VSMCs), fibroblasts, endothelial cells, immune cells (macrophages, T cells, B cells, and dendritic cells), and two types of rare cells, including neural cells and erythrocyte cells. Seurat clustering analysis identified four smooth muscle cell (SMC) subpopulations and five monocyte/macrophage subpopulations, with distinct transcriptional profiles. During AAA progression, three major SMC subpopulations were proportionally decreased, whereas the small subpopulation was increased, accompanied with down-regulation of SMC contractile markers and up-regulation of pro-inflammatory genes. Another AAA-associated cellular response is immune cell expansion, particularly monocytes/macrophages. Elastase exposure induced significant expansion and activation of aortic resident macrophages, blood-derived monocytes and inflammatory macrophages. We also identified increased blood-derived reparative macrophages expressing anti-inflammatory cytokines suggesting that resolution of inflammation and vascular repair also persist during AAA progression. Conclusion Our data identify AAA disease-relevant transcriptional signatures of vascular cells in the IAA. Furthermore, we characterize the heterogeneity and cellular responses of VSMCs and monocytes/macrophages during AAA progression, which provide insights into their function and the regulation of AAA onset and progression.

scholarly journals Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain studied at single-cell resolution

2019 ◽  
Vol 116 (18) ◽  
pp. 9103-9114 ◽  
Author(s):  
Jacob S. Heng ◽  
Amir Rattner ◽  
Genevieve L. Stein-O’Brien ◽  
Briana L. Winer ◽  
Bryan W. Jones ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Single Cell ◽  
Rna Sequencing ◽  
Chronic Hypoxia ◽  
Muller Glia ◽  
Müller Glia ◽  
Cell Type ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific

The mammalian CNS is capable of tolerating chronic hypoxia, but cell type-specific responses to this stress have not been systematically characterized. In the Norrin KO (NdpKO) mouse, a model of familial exudative vitreoretinopathy (FEVR), developmental hypovascularization of the retina produces chronic hypoxia of inner nuclear-layer (INL) neurons and Muller glia. We used single-cell RNA sequencing, untargeted metabolomics, and metabolite labeling from 13C-glucose to compare WT and NdpKO retinas. In NdpKO retinas, we observe gene expression responses consistent with hypoxia in Muller glia and retinal neurons, and we find a metabolic shift that combines reduced flux through the TCA cycle with increased synthesis of serine, glycine, and glutathione. We also used single-cell RNA sequencing to compare the responses of individual cell types in NdpKO retinas with those in the hypoxic cerebral cortex of mice that were housed for 1 week in a reduced oxygen environment (7.5% oxygen). In the hypoxic cerebral cortex, glial transcriptome responses most closely resemble the response of Muller glia in the NdpKO retina. In both retina and brain, vascular endothelial cells activate a previously dormant tip cell gene expression program, which likely underlies the adaptive neoangiogenic response to chronic hypoxia. These analyses of retina and brain transcriptomes at single-cell resolution reveal both shared and cell type-specific changes in gene expression in response to chronic hypoxia, implying both shared and distinct cell type-specific physiologic responses.

scholarly journals Preparation of single cell suspensions enriched in mouse brain vascular cells for single-cell RNA sequencing

2021 ◽  
Vol 2 (3) ◽  
pp. 100715
Author(s):  
Akari Yamazaki ◽  
Francis Shue ◽  
Yu Yamazaki ◽  
Yuka A. Martens ◽  
Guojun Bu ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Mouse Brain ◽  
Cell Suspensions ◽  
Vascular Cells ◽  
Single Cell Rna Sequencing

scholarly journals Single-cell analysis of salt-induced hypertensive mouse aortae reveals cellular heterogeneity and state changes

2021 ◽  
Author(s):  
Ka Zhang ◽  
Hao Kan ◽  
Aiqin Mao ◽  
Li Geng ◽  
Xin Ma
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Salt Intake ◽  
High Salt ◽  
Gene Set Enrichment Analysis ◽  
Cellular Heterogeneity ◽  
Vascular Cells ◽  
Mesenchymal Transition ◽  
Single Cell Rna Sequencing

AbstractElevated blood pressure caused by excessive salt intake is common and associated with cardiovascular diseases in most countries. However, the composition and responses of vascular cells in the progression of hypertension have not been systematically described. We performed single-cell RNA sequencing on the aortic arch from C57BL/6J mice fed a chow/high-salt diet. We identified 19 distinct cell populations representing 12 lineages, including smooth muscle cells (SMCs), fibroblasts, endothelial cells (ECs), B cells, and T cells. During the progression of hypertension, the proportion of three SMC subpopulations, two EC subpopulations, and T cells increased. In two EC clusters, the expression of reactive oxygen species-related enzymes, collagen and contractility genes was upregulated. Gene set enrichment analysis showed that three SMC subsets underwent endothelial-to-mesenchymal transition. We also constructed intercellular networks and found more frequent cell communication among aortic cells in hypertension and that some signaling pathways were activated during hypertension. Finally, joint public genome-wide association study data and our single-cell RNA-sequencing data showed the expression of hypertension susceptibility genes in ECs, SMCs, and fibroblasts and revealed 21 genes involved in the initiation and development of high-salt-induced hypertension. In conclusion, our data illustrate the transcriptional landscape of vascular cells in the aorta associated with hypertension and reveal dramatic changes in cell composition and intercellular communication during the progression of hypertension.

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