Transcriptional profiling of the Arabidopsis root quiescent center
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Idan Efroni
PROVIDER: E-GEOD-64253 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the WOX5 marker. To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5.
2014-12-17 | GSE64253 | GEO
Project description:Insulin resistance is necessary but not sufficient for the development of type 2 diabetes. Diabetes results when pancreatic beta-cells fail to compensate for insulin resistance by increasing insulin production through an expansion of beta-cell mass or increased insulin secretion. Communication between insulin target tissues and beta-cells may initiate this compensatory response. Correlated changes in gene expression between tissues can provide evidence for such intercellular communication. We profiled gene expression in six tissues of mice from an obesity-induced diabetes-resistant and a diabetes-susceptible strain before and after the onset of diabetes. We studied the correlation structure of mRNA abundance and identified 105 co-expression gene modules. We provide an interactive gene network model showing the correlation structure between the expression modules within and among the six tissues. This resource also provides a searchable database of gene expression profiles for all genes in six tissues in lean and obese diabetes-resistant and diabetes-susceptible mice, at 4 and 10 weeks of age. A cell cycle regulatory module in islets predicts diabetes susceptibility. The module predicts islet replication; we found a strong correlation between ^2 H_2 O incorporation into islet DNA /in vivo/ and the expression pattern of the cell cycle module. This pattern is highly correlated with that of several individual genes in insulin target tissues, including IGF2, which has been shown to promote beta-cell proliferation, suggesting that these genes may provide a link between insulin resistance and beta-cell proliferation. Keywords: time course, mouse strain comparison, effect of obesity, Type 2 diabetes is a disorder that involves an increased demand for insulin brought about by insulin resistance, together with a failure to compensate with sufficient insulin production. Although Insulin resistance occurs in most obese individuals, diabetes is generally forestalled through compensation with increased insulin. This increase in insulin occurs through an expansion of beta-cell mass and/or increased insulin secretion by individual beta-cells. Failure to compensate for insulin resistance leads to type 2 diabetes. One way to understand the pathophysiology of diabetes is to examine the coordinate changes in gene expression that occur in insulin-responsive tissues and pancreatic islets in obese animals that either compensate for insulin resistance or progress to type 2 diabetes. In each case, there are groups of genes that undergo changes in expression in a highly correlated fashion. By identifying groups of correlated transcripts (gene expression modules) during the compensation and development of diabetes, we can gain insight into potential pathways and regulatory networks in obesity-induced diabetes. We study two strains of mice that differ in obesity-induced diabetes susceptibility. In this study, we surveyed gene expression in six tissues of lean and obese C57BL/6 (B6) and BTBR mice aged 4 wks and 10 wks. B6 mice remain essentially non-diabetic at all ages, irrespective of obesity. When obese, BTBR mice become severely diabetic by 10 weeks of age. By analyzing the correlation structure of the genes under three contrast conditions, obesity, strain, and age, we identified gene expression modules associated with the onset of diabetes and provide an interactive co-expression network model of type 2 diabetes. We found a key module that is comprised of cell cycle regulatory genes. In the islet, the expression profile of these transcripts accurately predicts diabetes and is highly correlated with islet cell proliferation.
2008-03-14 | E-GEOD-10785 | biostudies-arrayexpress
Project description:131 human cancer cell lines' mRNA expression profiles have been characterized. Keywords: Cell Line Comparison mRNA samples obtained from 131 human cancer cell lines were hybridized to Agilent Human 3.0 A1 arrays and gene expression (mlratio) was measured relative to a common reference RNA pool (Human Universal Reference RNA, Stratagene, La Jolla, CA).
2010-06-25 | E-GEOD-13598 | biostudies-arrayexpress
Project description:To uncover the genetic determinants affecting expression in a metabolically active tissue relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting greater than 40,000 transcripts and genotyped DNA from each of these samples at greater than 1,000,000 SNPs. The relatively large sample size of this study and the large number of SNPs genotyped provided the means to assess the relationship between genetic variants and gene expression and it provided this look for the first time in a non-blood derived, metabolically active tissue. A comprehensive analysis of the liver gene expression traits revealed that thousands of these traits are under the control of well defined genetic loci, with many of the genes having already been implicated in a number of human diseases. Clincal data was requested, but not provided by submitter. Keywords: eQTL Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.
2008-05-07 | E-GEOD-9588 | biostudies-arrayexpress
Project description:The metabolic impact of the common peroxisome proliferator-activated receptor gamma isoform 2 (PPARγ2) variant Pro12Ala in human populations has been widely debated. We demonstrate using a Pro12Ala knock-in model that on chow Ala/Ala mice are leaner, have improved insulin sensitivity and plasma lipid profiles, and longer lifespan. Gene-environment interactions played a key role as high-fat feeding eliminated the beneficial effects of the Pro12Ala variant on adiposity, plasma lipids, and insulin sensitivity. The underlying molecular mechanisms involve changes in cofactor interaction and adiponectin signaling. Altogether, our results establish the Pro12Ala variant of Pparγ2 as an important modulator in metabolic control that strongly depends on the metabolic context. Pparγ Pro12Ala and wild-type littermates were fed regular rodent chow or high-fat diet (D12330, 5560 kcal/kg, Research Diets, New Brunswick, NJ), as indicated. Only males were used to minimize possible effects of variation in estrus status of females. Since the body weight development of Pro/Ala heterozygote mice was intermediate to that of Pro/Pro and Ala/Ala mice, we focused on the two homozygote genotypes in further experimentation. Mice were housed with a 12h light-dark cycle and had free access to water and food. Eight week old male Pro/Pro and Ala/Ala littermate mice were fed either regular rodent chow or high-fat diet (as above) for 15 weeks (n = 8-10 per group), at which time blood and tissue samples were collected. Total RNA extraction, sample amplification, labeling, and microarray (Genechip Mouse Genome 430 2.0 Array, Affymetrix Inc., Santa Clara, CA) processing steps were performed by the Rosetta Inpharmatics Gene Expression Laboratory (Seattle, WA) using custom automated procedures in compliance with manufacturer protocols. Microarray data was processed using Rosetta Resolver (Rosetta Inpharmatics, Seattle, WA) and expressed as relative to the virtual pool of HFD â Pro/Pro group (mlratio). Gene expression signatures were generated from these mlratios for expressed genes (25% of RMA processed intensities above 60% quantile) by T-testing (Pro/Pro vs. Ala/Ala) and correcting for multiple testing (20% cut-off for False Discovery Rate). GSEA was performed according to provider suggestions, Pro/Pro vs. Ala/Ala. Statistical significance was declared if P < 0.05.
2010-06-25 | E-GEOD-13305 | biostudies-arrayexpress
Project description:COPD is a common and disabling lung disease for which very few therapeutic options are currently available. We reasoned that global gene expression profiling of COPD lungs could reveal previously unidentified disease pathways for potential therapeutic interventions. Forty-eight human lung samples were obtained from lungs or lobes resected for small peripheral lung lesions (5 non-smokers, 21 GOLD 0, 9 GOLD 1, 10 GOLD 2 and 3 GOLD 3 patients). mRNA from the specimens was profiled using Agilent’s Functional ID v2.0 array which contains 23,720 sequences. Quantitative morphometric analysis of the specimens revealed that the samples contained a variable proportion of airways, blood vessels and parenchyma. Incorporating these data into a model relating gene expression to % predicted forced expiratory flow between 25 and 75% of forced expiratory volume (FEF 25-75 % P) revealed a signature gene set of 203 transcripts. Genes involved in extracellular matrix synthesis/degradation, oxidative stress and cell proliferation were among the up-regulated genes whereas genes which participate in nicotine metabolism, elastic fiber homeostasis and anti-inflammatory response were down-regulated. Immunohistochemistry confirmed expression of urokinase (PLAU), urokinanse receptor (PLAUR) and thrombospondin (THBS1) by alveolar macrophages and small airway epithelial cells. Genes in this pathway have been shown to be involved in transforming growth factor beta-1 (TGF?1) and matrix metalloproteinase (MMP) activation and are subject to inhibition by serpin E2. Interestingly, both TGF?1 and serpin E2 have been identified as candidate genes in COPD genetic linkage and association studies. The results thus provide a possible link between these two powerful approaches to identify potential therapeutic targets. (255 words) Forty-eight human lung samples were obtained from lungs or lobes resected for small peripheral lung lesions (5 non-smokers, 21 GOLD 0, 9 GOLD 1, 10 GOLD 2 and 3 GOLD 3 patients). mRNA from the specimens was profiled using Agilent’s Functional ID v2.0 array which contains 23,720 sequences. Quantitative morphometric analysis of the specimens revealed that the samples contained a variable proportion of airways, blood vessels and parenchyma. Incorporating these data into a model relating gene expression to % predicted forced expiratory flow between 25 and 75% of forced expiratory volume (FEF 25-75 % P) revealed a signature gene set of 203 transcripts.
2007-11-09 | E-GEOD-8500 | biostudies-arrayexpress
Project description:Murine hematopoietic stem cells were sorted by FACS from C57BL/6 Evi1+/GFP mice. Gene expression profiles of LSKCD41–CD48–CD150+CD34+ cells, LSKCD41–CD48–CD150+CD34–Evi1-GFP– cells, and LSKCD41–CD48–CD150+CD34–Evi1-GFP+ cells were generated.
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Project description:RNAseq of germinal center B cells with different Blimp-1-GFP reporter level. Sorted germinal center populations were defined by their expression of Blimp-1-GFP reporter and the cell surface marker CD138 before they were further split into dark zone or light zone / dark zone like or light zone like cells based on their expression of the surface marker CXCR4 and CD83. We used RNAseq to find genes differentially regulated in various Blimp-1-GFP expressing germinal center populations from the spleen at day 10 after intraperitoneal immunisation with sheep red blood cells.
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