scholarly journals Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Hui Du ◽  
Juan Shi ◽  
Ming Wang ◽  
Shuhong An ◽  
Xingjing Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Rna Sequencing ◽  
Dorsal Horn ◽  
Chronic Constriction Injury ◽  
Expression Profiles ◽  
Gene Expression Profiles

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 Microbial single-cell RNA sequencing by split-pool barcoding

Science ◽  
2020 ◽  
Vol 371 (6531) ◽  
pp. eaba5257 ◽  
Author(s):  
Anna Kuchina ◽  
Leandra M. Brettner ◽  
Luana Paleologu ◽  
Charles M. Roco ◽  
Alexander B. Rosenberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput ◽  
Single Cell Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Growth Stages ◽  
High Throughput Analysis ◽  
Single Cell Rna Sequencing

Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive bacteria that can resolve heterogeneous transcriptional states. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating an atlas of changes in metabolism and lifestyle. We retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction and also identified unexpected gene expression states, including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities that are otherwise not amenable to single-cell analysis, such as natural microbiota.

scholarly journals The origin, fate and function of macrophages in the peripheral nervous system—an update

2020 ◽  
Vol 32 (11) ◽  
pp. 709-717 ◽  
Author(s):  
Lukas Amann ◽  
Marco Prinz
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Rna Sequencing ◽  
Peripheral Nervous System ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
New Techniques ◽  
Macrophage Populations ◽  
And Function ◽  
First Time

Abstract The field of macrophage biology has made enormous progress over recent years. This was triggered by the advent of several new techniques such as the establishment of Cre/loxP-based transgenic mouse models that allowed for the first time delineation of the ontogeny and function of specific macrophage populations across many tissues. In addition, the introduction of new high-throughput technologies like bulk RNA sequencing and later single-cell RNA sequencing as well as advances in epigenetic analysis have helped to establish gene expression profiles, enhancer landscapes and local signaling cues that define and shape the identity of diverse macrophage populations. Nonetheless, some macrophage populations, like the ones residing in the peripheral nervous system (PNS), have not been studied in such detail yet. Here, we discuss recent studies that shed new light on the ontogeny, heterogeneity and gene expression profiles of resident macrophages in peripheral nerves and described differential activation of macrophage subsets during and after acute sciatic nerve injury.

scholarly journals RNA Sequencing of the Human Milk Fat Layer Transcriptome Reveals Distinct Gene Expression Profiles at Three Stages of Lactation

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e67531 ◽  
Author(s):  
Danielle G. Lemay ◽  
Olivia A. Ballard ◽  
Maria A. Hughes ◽  
Ardythe L. Morrow ◽  
Nelson D. Horseman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Milk ◽  
Rna Sequencing ◽  
Milk Fat ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Distinct Gene ◽  
Three Stages ◽  
Human Milk Fat

scholarly journals G2S3: a gene graph-based imputation method for single-cell RNA sequencing data

2020 ◽  
Author(s):  
Weimiao Wu ◽  
Qile Dai ◽  
Yunqing Liu ◽  
Xiting Yan ◽  
Zuoheng Wang
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Sequencing Data ◽  
High Data ◽  
Study Gene Expression ◽  
Single Cell Rna Sequencing ◽  
Novel Method

AbstractSingle-cell RNA sequencing provides an opportunity to study gene expression at single-cell resolution. However, prevalent dropout events result in high data sparsity and noise that may obscure downstream analyses. We propose a novel method, G2S3, that imputes dropouts by borrowing information from adjacent genes in a sparse gene graph learned from gene expression profiles across cells. We applied G2S3 and other existing methods to seven single-cell datasets to compare their performance. Our results demonstrated that G2S3 is superior in recovering true expression levels, identifying cell subtypes, improving differential expression analyses, and recovering gene regulatory relationships, especially for mildly expressed genes.

scholarly journals A survey of the mouse hindbrain in the fed and fasted state using single-nucleus RNA sequencing

2021 ◽  
Author(s):  
Georgina K.C. Dowsett ◽  
Brian Y.H. Lam ◽  
John Tadross ◽  
Irene Cimino ◽  
Debra Rimmington ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Area Postrema ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fasted State ◽  
Single Nucleus ◽  
Human Use ◽  
Obesity Drugs

AbstractObjectiveThe area postrema (AP) and the nucleus tractus solitaris (NTS), located in the hindbrain, are key nuclei that sense and integrate peripheral nutritional signals and, consequently, regulate feeding behaviour. While single cell transcriptomics have been used in mice to reveal the gene expression profile and heterogeneity of key hypothalamic populations, similar in-depth studies have not yet been performed in the hindbrain.MethodsUsing single-nucleus RNA sequencing, we provide a detailed survey of 16,034 cells within the AP and NTS of the mouse, in the fed and fasted state.ResultsOf these, 8910 are neurons that group into 30 clusters, with 4289 coming from mice fedad libitumand 4621 from overnight fasted mice. 7124 nuclei are from non-neuronal cells, including oligodendrocytes, astrocytes and microglia. Interestingly, we identified that the oligodendrocyte population was particularly transcriptionally sensitive to an overnight fast. The receptors GLP1R, GIPR, GFRAL and CALCR, which bind GLP1, GIP, GDF15 and amylin respectively, are all expressed in the hindbrain and are major targets for anti-obesity therapeutics. We characterise the transcriptomes of these four populations and show that their gene expression profiles are not dramatically altered by an overnight fast. Notably, we find that roughly half of cells that express GIPR are oligodendrocytes. Additionally, we profile POMC expressing neurons within the hindbrain and demonstrate that 84% of POMC neurons express either PCSK1, PSCK2 or both, implying that melanocortin peptides are likely produced by these neurons.ConclusionWe provide a detailed single-cell level characterisation of AP and NTS cells expressing receptors for key anti-obesity drugs that are either already approved for human use or are in clinical trials. This resource will help delineate the mechanisms underlying the effectiveness of these compounds, and also prove useful in the continued search for other novel therapeutic targets.

scholarly journals SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references

2020 ◽  
Author(s):  
Meichen Dong ◽  
Aatish Thennavan ◽  
Eugene Urrutia ◽  
Yun Li ◽  
Charles M Perou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Rna Seq ◽  
Cell Type ◽  
Mixed Cell ◽  
Single Cell Rna Sequencing

Abstract Recent advances in single-cell RNA sequencing (scRNA-seq) enable characterization of transcriptomic profiles with single-cell resolution and circumvent averaging artifacts associated with traditional bulk RNA sequencing (RNA-seq) data. Here, we propose SCDC, a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expression profiles from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the problem of batch-effect confounding. SCDC is benchmarked against existing methods using both in silico generated pseudo-bulk samples and experimentally mixed cell lines, whose known cell-type compositions serve as ground truths. We show that SCDC outperforms existing methods with improved accuracy of cell-type decomposition under both settings. To illustrate how the ENSEMBLE framework performs in complex tissues under different scenarios, we further apply our method to a human pancreatic islet dataset and a mouse mammary gland dataset. SCDC returns results that are more consistent with experimental designs and that reproduce more significant associations between cell-type proportions and measured phenotypes.

Molecular signature of late-stage human ALS revealed by expression profiling of postmortem spinal cord gray matter

2004 ◽  
Vol 16 (2) ◽  
pp. 229-239 ◽  
Author(s):  
Fernando Dangond ◽  
Daehee Hwang ◽  
Sandra Camelo ◽  
Piera Pasinelli ◽  
Matthew P. Frosch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Gray Matter ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Terminal State ◽  
Molecular Signature ◽  
Fisher Discriminant Analysis ◽  
Sporadic Als

Little is known about global gene expression patterns in the human neurodegenerative disease amyotrophic lateral sclerosis (ALS). To address this, we used high-density oligonucleotide microarray technology to compare expression levels of ∼6,800 genes in postmortem spinal cord gray matter obtained from individuals with ALS as well as normal individuals. Using Fisher discriminant analysis (FDA) and leave-one-out cross-validation (LOOCV), we discerned an ALS-specific signature. Moreover, it was possible to distinguish familial ALS (FALS) from sporadic ALS (SALS) gene expression profiles. Characterization of the specific genes significantly altered in ALS uncovered a pro-inflammatory terminal state. Moreover, we found alterations in genes involved in mitochondrial function, oxidative stress, excitotoxicity, apoptosis, cytoskeletal architecture, RNA transcription and translation, proteasomal function, and growth and signaling. It is apparent from this study that DNA microarray analysis and appropriate bioinformatics can reveal distinct phenotypic changes that underlie the terminal stages of neurodegeneration in ALS.

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