Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LXR activation induces insulin resistance in primary human adipocytes

ABSTRACT: The effects of LXR stimulation by GW3965 treatment on global mRNA and miRNA expression in primary human in vitro differentiated adipocytes was investigated using microarray profiling. Preadipocytes were isolated from human adipose tissue obtained from healthy subjects and differentiated in vitro. Around day 11 of differentiation cells were treated with the Liver X Receptor agonist GW3865 for 24 h and lysed. Total RNA as prepared and hybridised biotinylated complementary RNA to Gene 1.0 ST Arrays using standardized protocols (Affymetrix Inc., Santa Clara, CA). The GeneChip Operating Software Version 1.4 was used for analysis. Arrays were normalized using PLIER and all samples were subjected to an all-probeset scaling-to-target signal of 100. Preadipocytes were isolated from human adipose tissue obtained from healthy subjects and differentiated in vitro. Around day 11 of differentiation cells were treated with the Liver X Receptor agonist GW3865 for 12 h and lysed. Total RNA was prepared and and labelled using the FlashTag biotin HSR labeling kit (Genisphere Inc., Hatfield, PA) according to the supplier's protocol. The labelled samples were placed in a hybridization cocktail mix containing 4% formamide and hybridised overnight to Affymetrix miRNA Arrays (Affymetrix Inc.) following the indicated Genisphere protocol. The arrays were washed, stained and scanned in an Affymetrix GCS 3000 scanner. Signal intensities and present calls were generated by using the microRNA QC tool by Affymetrix using default settings i.e. Background Adjustment: BC-CG adjust, Normalization: Quantile: Summarization: Median Polish.

ORGANISM(S): Homo sapiens

SUBMITTER: Annie Pettersson

PROVIDER: E-GEOD-41223 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [miRNA data]

Project description:We used an unbiased systems biology approach to study the regulation of gene expression in human adipose tissue focusing on inflammation. We show that microRNAs play a major role as regulators of CCL2 production in obesity. Abdominal subcutaneous adipose needle biopsies were obtained from women (n=56) with a wide variation in BMI. From the biopsies, total RNA was isolated and labelled using the FlashTag biotin HSR labeling kit (Genisphere Inc., Hatfield, PA) according to the supplier's protocol. The labelled samples were placed in a hybridization cocktail mix containing 4% formamide and hybridised overnight to Affymetrix miRNA Arrays (Affymetrix Inc.) following the indicated Genisphere protocol. The arrays were washed, stained and scanned in an Affymetrix GCS 3000 scanner. Signal intensities and present calls were generated by using the microRNA QC tool by Affymetrix.

2012-08-12 | E-GEOD-25470 | biostudies-arrayexpress

Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity (differentiation data)

Project description:We used an unbiased systems biology approach to study the regulation of gene expression in human adipose tissue focusing on inflammation. We show that microRNAs play a major role as regulators of CCL2 production in obesity. Subcutaneous adipose tissue was obtained from healthy subjects undergoing cosmetic liposuction (n=12). There was no selection for age, sex or BMI. From the tissue, we isolated preadipocytes and in vitro differentiated them to adipocytes. The cells were lysed at day 4/5 (early), 8 (middle) and 12 (late) of differentiation. From the samples, we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA). Pre-processing was performed using the Affymetrix Expression Console version 1.1 and the following settings: Summarization: PLIER; Background Correction: PM-GCBG; Normalization: Global Median.

2012-08-12 | E-GEOD-25910 | biostudies-arrayexpress

Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [gene expression]

Project description:We used an unbiased systems biology approach to study the regulation of gene expression in human adipose tissue focusing on inflammation. We show that microRNAs play a major role as regulators of CCL2 production in obesity. Abdominal subcutaneous adipose needle biopsies were obtained from women (n=56) with a wide variation in BMI. From the biopsies we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA), labelled RNA to Affymetrix miRNA arrays, and bisulphite converted DNA to Illumina Infinium HumanMethylation27 beadchips using standardised protocols (Affymetrix Inc., Illumina Inc.) . Subsequent analyses of gene expression was performed using the Affymetrix GeneChip Operating Software version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probeset scaling-to-target signal of 100.

2012-08-12 | E-GEOD-25401 | biostudies-arrayexpress

Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity

Project description:This SuperSeries is composed of the following subset Series: GSE25401: Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [gene expression] GSE25470: Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [miRNA data] GSE25910: Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [differentiation data] Refer to individual Series

2012-08-12 | E-GEOD-25402 | biostudies-arrayexpress

Effect of Healthy Nordic diet on gene expression in peripheral blood mononuclear cells

Project description:In a randomized controlled dietary intervention study we compared an isocaloric Healthy Nordic diet with the average Nordic diet for influence on peripheral blood mononuclear cells (PBMC) gene expression. We studied obese adults with features of the metabolic syndrom, n=66. There was no significant difference in age, BMI, or gene expression between the groups before the intervention. The intervention lasted for 18-24 weeks. Blood samples were obtained before (W0), during (W12) and after completion (W18-24) of the dietary intervention. From the samples we extracted RNA. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix Inc.).

2015-05-13 | E-GEOD-68759 | biostudies-arrayexpress

Influence of dietary fatty acid composition on white adipose tissue gene expression in humans

Project description:In a randomized controlled dietary intervention study, we compared a diet enriched in polyunsaturated fatty acids (PUFA) with a diet enriched in saturated fatty acids (SFA) for influence on abdominal subcutaneous adipose tissue gene expression. We studied young lean adults; 11 women and 25 men. There was no significant difference in age, BMI, or gene expression between the PUFA and SFA groups before the intervention. The intervention lasted for seven weeks. We calculated for each gene the absolute difference in gene expression after vs. before intervention (deltas), and compared the deltas between the PUFA and SFA group using SAM. 12 genes were significantly differentially regulated by the two diets with a FDR of 25%. These include metabolic and adipokine genes. In conclusion, dietary fatty acids have a modest influence on white adipose tissue gene expression. Abdominal subcutaneous adipose needle biopsies were obtained from young adults before (W0) and after completion (W7) of the dietary intervention. From the biopsies we extracted RNA. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix, Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix, Inc.). Signicance analysis of microarrays (SAM) was use to compare the difference in gene expression between groups.

2014-07-01 | E-GEOD-43642 | biostudies-arrayexpress

A healthy Nordic diet has a beneficial influence on the expression of genes involved in inflammation in subcutaneous adipose tissue

Project description:In a randomized controlled dietary intervention study we compared an isocaloric Healthy Nordic diet with the average Nordic diet for influence on abdominal subcutaneous adipose tisse gene expression. We studied obese adults with features of the metabolic syndrom, n=56. There was no significant difference in age, BMI, or gene expression between the groups before the intervention. The intervention lasted for 18-24 weeks. Gene expression was analyzed using linear mixed-effects models including specific genes as dependent variable, subject identifier as a random effect, and body weight, age, gender, study centre (i.e. also study duration), study group, time-point and study group * time-point interaction as covariates. 128 genes were significantly different regulated by the two diets with a FDR of 24%. TThese genes were overrepresented in pathways related to immune response. I conclusion, a Healthy Nordic diet reduces inflammatory gene expression in abdominal subcutaneous adipose tissue. This could contribute to beneficial influences on lipid metabolism and cardiovascular disease. Abdominal subcutaneous adipose needle biopsies were obtained before (W0) and after completion (W18-24) of the dietary intervention. From the biopsies we extracted RNA. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix Inc.).

2015-01-26 | E-GEOD-56716 | biostudies-arrayexpress

Role of milk fat globule membrane (MFGM) in modulating gene expression in humans

Project description:The aim of this study was to investigate if milk fat globule membrane (MFGM) enclosing the dairy fat influence peripheral blood mononuclear cells (PBMC) gene expression. This study was a 8-week single-blind, randomized, controlled isocaloric trial with two parallel groups including overweight (mean BMI: 28) adult women (n=30). All subjects consumed 40 g dairy fat per day either as cream (MFGM diet) or as butter oil (control diet). MFGM diet and control diet showed differential responses in plasma cholesterol. Absolute differences in gene expression were calculated for each gene in each subject, comparing after with before the intervention. These absolute differences in gene expression were compared between intervention groups with T-test and with Significance Analysis of Microarrays (SAM). 19 genes were significantly different regulated by the two diets with a FDR of 23%. Most of thechanges in gene expression correlated with changes in blood lipids. Patients were examined in the morning after 12 h's fasting. Whole blood was obtained before (W0) and after completion (W8) of the dietary intervention for isolation of PBMCs and RNA extraction. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix Inc.). Signicance analysis of microarrays (SAM) was use to compare the difference in gene expression between groups.

2015-08-01 | E-GEOD-60148 | biostudies-arrayexpress

ADIPOSE TISSUE PATHWAYS INVOLVED IN WEIGHT LOSS OF CANCER CACHEXIA

Project description:The regulatory gene pathways underlying the loss of adipose tissue in cancer cachexia are unknown and were explored using pangenomic transcriptome profiling. Gene expression profiles (Human Gene 1.0 ST) of abdominal subcutaneous adipose tissue were studied in gastrointestinal cancer patients with (N=13) or without (N=14) cachexia. Data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4.

2010-04-10 | E-GEOD-20571 | biostudies-arrayexpress

Effects of DHA-rich n-3 fatty acid supplementation on gene expression in blood mononuclear leukocytes: the OmegAD study

Project description:The hypothesis was that 6 months of dietary n-3 FA supplementation to humans affected expression of genes that might be of significance for inflammatory processes and for Alzheimer´s disease. Effects on global gene expression profiles (Affymetrix Human Focus array) in human blood mononuclear leukocytes obtained from 11 patients with Alzheimer´s disease before and after 6 months of a DHA-rich n-3 fatty acid supplementation. Data analyses were performed using Gene chip Operating Software (GCOS) Version 1.4. Two Samples, GSM735991 and GSM736014, are missing CEL files due to storage failure.

2012-05-23 | E-GEOD-29680 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data