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The effect of intermittent hypoxia on gene expression in the liver of ob/ob mice

ABSTRACT: All animals were kept in a controlled environment (22-24 °C with a 12 h : 12 h light : dark cycle; lights on at 09.00) on a standard chow diet with free access to water. Five ob/ob mice (sample_ids GSM32865-GSM32869) were placed in the intermittent hypoxia (IH) chamber and subjected to IH for 12 consecutive weeks and compared to pair-fed control exposed to intermittent room (IA) air for 12 weeks in identical chambers (n = 5, sample_ids GSM32860-GSM32864). The IH and IA states were induced during the light phase alternating with 12 h of constant room air during the dark phase. The IH and IA groups were weight-matched daily during the experiment by varying food intake. Weight-matching was conducted in pairs. The signal intensity fluorescent images produced during samples hybridizations to Affymetrix GeneChip were read using the Agilent Gene Array Scanner and converted into GeneChip Cell files (CEL) using MAS 5.0 software (Affymetrix, Santa Clara, CA). Gene expression values were generated form CEL files using Robust Microarray Analysis (RMA, Bioconductor affy package). Briefly, the rma module of this package was used for background correction, across array normalization, and extraction of the probe level data. Ref: Irizarry R, Gautier L, and Cope L, An R package for analyses of Affymetrix oligonucleotide arrays. The Analysis of Gene Expression Data: Methods and Software, ed. G Parmigiani,ES Garrett, RA Irizarry,and SL Zeger. 2003, New York: Springer Keywords: ordered

ORGANISM(S): Mus musculus

PROVIDER: GSE1873 | GEO | 2004/10/27

SECONDARY ACCESSION(S): PRJNA90547

REPOSITORIES: GEO

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Transcription profiling of mouse liver to identify the effect of intermittent hypoxia on gene expression in the liver of ob/ob mice

Project description:All animals were kept in a controlled environment (22-24 °C with a 12 h : 12 h light : dark cycle; lights on at 09.00) on a standard chow diet with free access to water. Five ob/ob mice (sample_ids GSM32865-GSM32869) were placed in the intermittent hypoxia (IH) chamber and subjected to IH for 12 consecutive weeks and compared to pair-fed control exposed to intermittent room (IA) air for 12 weeks in identical chambers (n = 5, sample_ids GSM32860-GSM32864). The IH and IA states were induced during the light phase alternating with 12 h of constant room air during the dark phase. The IH and IA groups were weight-matched daily during the experiment by varying food intake. Weight-matching was conducted in pairs. The signal intensity fluorescent images produced during samples hybridizations to Affymetrix GeneChip were read using the Agilent Gene Array Scanner and converted into GeneChip Cell files (CEL) using MAS 5.0 software (Affymetrix, Santa Clara, CA). Gene expression values were generated form CEL files using Robust Microarray Analysis (RMA, Bioconductor affy package). Briefly, the rma module of this package was used for background correction, across array normalization, and extraction of the probe level data. Ref: Irizarry R, Gautier L, and Cope L, An R package for analyses of Affymetrix oligonucleotide arrays. The Analysis of Gene Expression Data: Methods and Software, ed. G Parmigiani,ES Garrett, RA Irizarry,and SL Zeger. 2003, New York: Springer

2007-11-01 | E-GEOD-1873 | biostudies-arrayexpress

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2015-04-17 | GSE59807 | GEO

Gene expression in the GWAT of ob/ob and ob/ob/Fsp27-/- mice

2015-04-17 | E-GEOD-59807 | biostudies-arrayexpress

Gene Expression in the BAT and WAT of ob/ob and ob/ob/Cidea-/-/Cidec-/- mice

Project description:ob/ob mice is an obese mice. CIDE family proteins including Cidea, Cideb and Cidec play important role in lipid metabolism. Cidea is mainly expressed in the brown adipose tissue (BAT). Cidec is mainly expressed in the BAT and white adipose tissue (WAT). We generated ob/ob/Cidea-/-/Cidec-/- mice to investigate the phenotype of fat tissue. ob/ob/Cidea-/-/Cidec-/- mice are lean when compared with ob/ob mice. The tissue weight and TAG content of BAT and WAT was extreamly decreased in ob/ob/Cidea-/-/Cidec-/- mice compared with that in ob/ob mice. We next extract the total RNA from the BAT and WAT of ob/ob and ob/ob/Cidea-/-/Cidec-/- mice, to perform microarray analysis using Mouse Gene 1.0 ST array system, Affymetrix. We then analysised the up-regulated and down regulated pathways.

2018-04-18 | GSE100989 | GEO

Gene expression in livers of Lepob/ob (ob/ob) mice v.s. wild type C57BL/6J mice

Project description:To identify novel transcriptional factors involved in dysfunctional hepatic lipids homeostasis in obesity, mRNA microarray analysis were performed to of livers of ob/ob mice, a widely used obese model, and C57BL/6J control mice. Chow-fed ob/ob and C57BL/6J mice were housed in a 12 h of light and 12 h of dark cycle and fed ad libitum a regular chow diet. Mice were sacrificed at 16:00 (Zeitgeber Time 8 during light phase). Total RNA was prepared from each liver using TRIzol (Invitrogen). Equal aliquots of total RNA from each of four mouse livers in each group were pooled and used for biotin labeling as described in the Affymetrix technical bulletin. Then the transcriptional profiles of samples were probed using the Gene-Chip Mouse Genome 430 2.0 arrays.

2014-06-29 | E-MTAB-2678 | biostudies-arrayexpress

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2022-11-21 | GSE218086 | GEO

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Low dose Leptin (25 ng/hr and 12.5 ng/hr) in ob/ob mice

Project description:Ob/ob mice were given 0, 12.5 or 25 ng/hr leptin through an osmotic pump. After 12 days, livers RNA was prepared and illumina microarrays were done. We tested whether leptin can ameliorate diabetes independent of weight loss by defining the lowest dose at which leptin treatment of ob/ob mice reduces plasma [glucose] and [insulin]. We found that a leptin dose of 12.5 ng/hour significantly lowers blood glucose and that 25 ng/hour of leptin normalizes plasma glucose and insulin without significantly reducing body weight, thus establishing that leptin exerts its most potent effects on glucose metabolism. To find possible mediators of this effect, we profiled liver mRNA using microarrays and identified IGF Binding Protein 2 as being regulated by leptin with a similarly high potency. Over-expression of IGFBP2 by an adenovirus reversed diabetes in insulin resistant ob/ob, Ay/a and diet-induced obese mice (DIO), as well as insulin deficient streptozotocin-treated mice. Hyperinsulinemic clamp studies showed a three-fold improvement in hepatic insulin sensitivity following IGFBP2 treatment in ob/ob mice. These results show that IGFBP2 can regulate glucose metabolism, a finding with potential implications for the pathogenesis and treatment of diabetes.

2009-11-25 | GSE19185 | GEO

Expression Profiling of Livers From Female FC-ob Mice and MRKO-ob Mice

Project description:Objective: To investigate the effects of myeloid MR deletion on hepatic gene expression profiles in female mice Methods: 12-week old female FC-ob and MRKO-ob mice were euthanized and livers were collected and snap-frozen with liquid nitrogen. Total RNA were extracted using Trizol. After assessing the RNA quality with an Agilent 2000 Bioanalyzer, cDNA library was constructed using TruSeq RNA-Seq Sample Prep Kits. Deep sequencing was carried out on Illumina HiSeq 2000. Different gene expressions were confirmed by QRT-PCR. Results: With RNA-seq data, we identified 24 genes that differently expressed in MRKO-ob mice compared to FC-ob group. Confirmation with QRT-PCR revealed that the differently expressed genes were closely associated with hepatic steatosis, especially de novo lipogenesis. Conclusions: Our study investigated for the first time the gene expression profiles of female ob/ob mice with or without myeloid MR ablation. These findings provided clues to explore the mechanisms underlied the crosstalk between macrophages and hepatocytes in females. These findings have provided new knowledge basis for potential new strategies to treat or prevent NAFLD and T2DM.

2016-09-20 | GSE73438 | GEO

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