Global gene expression patterns spanning 3T3-L1 preadipocyte differentiation

2004 ◽  
Vol 84 (3) ◽  
pp. 367-376 ◽  
Author(s):  
C. Hansen ◽  
A. Fu ◽  
C. Li ◽  
W. T. Dixon ◽  
R. Christopherson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Adipocyte Differentiation ◽  
Expression Patterns ◽  
Subcutaneous Fat ◽  
Global Gene Expression ◽  
Differentiation Process ◽  
Comprehensive Overview ◽  
Self Organizing Maps ◽  
Som Clustering

Adipogenesis is of significant relevance from an agricultural perspective. Traits such as subcutaneous fat thickness, marbling and waste fat are of substantial economic importance in animal production. In order to discover more about the genetic basis of this process, a study was undertaken to examine the changes that occur daily in global gene expression as 3T3-L1 cells differentiate from preadipocyte to adipocyte. Duplicate RNA samples were collected daily during the differentiation process and probed with the Affymetrix U74Av2 GeneChip® microarray to allow the time-course analysis of the gene expression profile in these differentiating cells. Self-organizing maps (SOM) clustering was performed to extract patterns of expression over the course of the experiment (day 0 to day 6). The clustering generated nine distinct expression patterns containing between 74 and 420 genes/ESTs. Functional clusters and important chronological changes in the expression of key genes and gene groups were identified. The pattern of expression observed for many genes not only confirmed what has been shown previously for the early stages of differentiation, but also expanded this pattern to cover the whole differentiation process thus giving a very comprehensive overview of patterns and changes in gene expression over the time course of adipocyte differentiation. Key words: Adipocyte differentiation, gene expression, SOM clustering

Angiotensinogen gene expression in 3T3-L1 cells

1989 ◽  
Vol 256 (2) ◽  
pp. C448-C451 ◽  
Author(s):  
J. A. Saye ◽  
L. A. Cassis ◽  
T. W. Sturgill ◽  
K. R. Lynch ◽  
M. J. Peach
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Drug Treatment ◽  
Time Course ◽  
Adipocyte Differentiation ◽  
Drug Regimen ◽  
Mrna Levels ◽  
Differentiation Process ◽  
Clonal Cell Line ◽  
Angiotensinogen Gene

It has previously been established that angiotensinogen mRNA is present in brown and white adipose tissue of the rat. To determine whether angiotensinogen gene expression is present in adipocytes as compared with other cell elements, we have examined angiotensinogen mRNA in 3T3-L1 cells. These cells undergo adipocyte differentiation when the culture reaches confluence. To accelerate the differentiation process, cells were treated with dexamethasone and isobutylmethylxanthine for 3 days. On the 7th day after drug treatment, RNA was extracted from cells and was examined for angiotensinogen mRNA using a full-length rat angiotensinogen cDNA. Angiotensinogen mRNA was readily detected in differentiated 3T3-L1 cells. To determine when the gene is expressed, a 7-day time course from day 0 (before drug treatment) to day 7 was examined for the presence of angiotensinogen mRNA. In addition, C2 cells, a clonal cell line that does not differentiate into adipocytes, were examined. Angiotensinogen mRNA was detected on days 2-7 after drug treatment in 3T3-L1 cells, with no detectable levels in untreated 3T3-C2 cells. When 3T3-C2 cells were subjected to the same drug regimen, angiotensinogen mRNA levels increased in the same time course as 3T3-L1 cells. However, the increase in angiotensinogen message was greater in differentiating 3T3-L1 cells than in the nondifferentiating 3T3-C2 cells. Thus angiotensinogen mRNA is present in both adipocytes and in fibroblast-like cells and appears to be regulated by steroids.

Microarray analysis of global changes in gene expression during cardiac myocyte differentiation

2002 ◽  
Vol 9 (3) ◽  
pp. 145-155 ◽  
Author(s):  
Chang-Fu Peng ◽  
Yi Wei ◽  
Jeffrey M. Levsky ◽  
Thomas V. McDonald ◽  
Geoffrey Childs ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cardiac Myocytes ◽  
Large Scale ◽  
Time Course ◽  
Cardiac Myocyte ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Global Changes ◽  
Novel Genes ◽  
Myocyte Differentiation

Significant progress has been made in defining pathways that mediate the formation of the mammalian heart. Little is known, however, about the genetic program that directs the differentiation of cardiac myocytes from their precursor cells. A major hindrance to this kind of investigation has been the absence of an appropriate cell culture model of cardiac myocyte differentiation. Recently, a subline of P19 cells (P19CL6) was derived that, following dimethyl sulfoxide (DMSO) treatment, differentiate efficiently over 10 days into spontaneously beating cardiac myocytes. We demonstrate that these cells are indeed cardiac myocytes as they express cell type-specific markers and exhibit electrophysiological properties indicative of cardiac myocytes. The requirement for DMSO stimulation in this paradigm was shown to be limited to the first 4 days, suggesting that critical events in the differentiation process occur over this interval. To uncover relationships among known genes and identify novel genes that mediate cardiac myocyte differentiation, a detailed time course of changes in global gene expression was carried out using cDNA microarrays. In addition to the activation of genes encoding cardiac transcription factors and structural proteins, increases were noted in the expression of multiple known genes and expressed sequence tags (ESTs). Analysis of the former suggested the involvement of a variety of signaling pathways in cardiac myocyte differentiation. The 16 ESTs whose expression was increased during the early, stimulus-dependent phase of cardiac myocyte differentiation may be novel regulators of this process. Thus this first report of large-scale changes in gene expression during cardiac myocyte differentiation has delineated relationships among the expression patterns of known genes and identified a number of novel genes that merit further study.

A Global Vista of the Epigenomic State of the Mouse Submandibular Gland

2021 ◽  
pp. 002203452110120
Author(s):  
C. Gluck ◽  
S. Min ◽  
A. Oyelakin ◽  
M. Che ◽  
E. Horeth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Submandibular Salivary Gland ◽  
Data Sets ◽  
Control Mechanisms ◽  
Chromatin Immunoprecipitation Sequencing

The parotid, submandibular, and sublingual glands represent a trio of oral secretory glands whose primary function is to produce saliva, facilitate digestion of food, provide protection against microbes, and maintain oral health. While recent studies have begun to shed light on the global gene expression patterns and profiles of salivary glands, particularly those of mice, relatively little is known about the location and identity of transcriptional control elements. Here we have established the epigenomic landscape of the mouse submandibular salivary gland (SMG) by performing chromatin immunoprecipitation sequencing experiments for 4 key histone marks. Our analysis of the comprehensive SMG data sets and comparisons with those from other adult organs have identified critical enhancers and super-enhancers of the mouse SMG. By further integrating these findings with complementary RNA-sequencing based gene expression data, we have unearthed a number of molecular regulators such as members of the Fox family of transcription factors that are enriched and likely to be functionally relevant for SMG biology. Overall, our studies provide a powerful atlas of cis-regulatory elements that can be leveraged for better understanding the transcriptional control mechanisms of the mouse SMG, discovery of novel genetic switches, and modulating tissue-specific gene expression in a targeted fashion.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

scholarly journals Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data

2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Qihua Tan ◽  
Mads Thomassen ◽  
Mark Burton ◽  
Kristian Fredløv Mose ◽  
Klaus Ejner Andersen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Correlation Coefficient ◽  
Parametric Analysis ◽  
Time Course ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Microarray Time Course ◽  
Time Course Data ◽  
Generalized Correlation ◽  
Non Parametric

AbstractModeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.

Mechanism of increased PLD1 gene expression during early adipocyte differentiation process of mouse cell line 3T3-L1

2009 ◽  
pp. n/a-n/a ◽  
Author(s):  
Siqiang Gao ◽  
Hiromi Ito ◽  
Masashi Murakami ◽  
Kayo Yoshida ◽  
Yoko Tagawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Adipocyte Differentiation ◽  
Mouse Cell ◽  
Differentiation Process ◽  
Mouse Cell Line

scholarly journals Alterations in global gene expression patterns resulting from 10 days of endurance training in humans

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Nigel Keith Stepto ◽  
Timothy John Burton ◽  
Therese Griersmith ◽  
David Powell ◽  
Benedict James Canny
Keyword(s):  
Gene Expression ◽  
Endurance Training ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Gene Expression Patterns

scholarly journals Global gene expression patterns in response to white patch syndrome: Disentangling symbiont loss from the thermal stress response in reef-building coral

2019 ◽  
Author(s):  
Carly D. Kenkel ◽  
Veronique J.L. Mocellin ◽  
Line K. Bay
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Thermal Stress ◽  
Stress Response ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Host Protein ◽  
Gene Expression Patterns ◽  
White Patch

AbstractThe mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing symbiont loss from the abiotic stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in P. lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of abiotic stress from expression patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. The meta-analysis revealed that expression patterns in WPS-affected tissues were significantly correlated with prior studies examining short-term thermal stress responses. This correlation was independent of symbiotic state, as the strongest correlations were found between WPS adults and both symbiotic adult and aposymbiotic coral larvae experiencing thermal stress, suggesting that the majority of expression changes reflect a non-specific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration, and highlights unique responses to bleaching in an anemone model which engages in a non-obligate symbiosis.

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