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Atlas Rat cDNA Expression Array - Zipf's Normalization

ABSTRACT: Five microarrays from a larger dataset used to demonstrate a normalization technique base on Zipf's law. The original data set was generated by using Atlas Rat cDNA microarrays (Clontech, 588 genes) probed with rat brain tissue, from control (cerebellum n=10, olive n=10) and harmaline treated (cerebellum n=10, olive n=9) animals. Microarrays were probed according to established protocols and exposed to imaging plates overnight (BAS-MS 2325) and scanned at a 50 m resolution on a FLA-3000G phosphoimager (Raytest, Germany). Image gridding was carried out using VisualGrid® software (http://www.gpc-biotech.com). Keywords: other

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE1509 | GEO | 2004/07/03

SECONDARY ACCESSION(S): PRJNA90837

REPOSITORIES: GEO

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Atlas Rat cDNA Expression Array - Zipf's Normalization

Project description:Five microarrays from a larger dataset used to demonstrate a normalization technique base on Zipf's law. The original data set was generated by using Atlas Rat cDNA microarrays (Clontech, 588 genes) probed with rat brain tissue, from control (cerebellum n=10, olive n=10) and harmaline treated (cerebellum n=10, olive n=9) animals. Microarrays were probed according to established protocols and exposed to imaging plates overnight (BAS-MS 2325) and scanned at a 50 m resolution on a FLA-3000G phosphoimager (Raytest, Germany). Image gridding was carried out using VisualGridÂ® software (http://www.gpc-biotech.com).

2010-06-06 | E-GEOD-1509 | biostudies-arrayexpress

Human UniGene Set RZPD 1 - Zipf's Normalization

Project description:Five microarrays from a larger dataset used to demonstrate a normalization technique base on Zipf's law. The original data-set generated using a global genome-wide cDNA clone set (Human UniGene clone set RZPD 1 - http://www.rzpd.de - Build 138, NCBI), which consisted of ~33,792 cDNA clone inserts spotted in duplicate onto membranes (18). These microarrays (n=31) were hybridized with 33P-labeled cDNA derived from total RNA extracted from biopsy material from the sigmoidal colon of normal (control, n=11), and patients with Crohn's disease (condition A, n=10) and ulcerative colitis (condition B, n=10). Microarrays were probed according to established protocols and exposed to imaging plates overnight (BAS-MS 2325) and scanned at a 50 m resolution on a FLA-3000G phosphoimager (Raytest, Germany). Image gridding was carried out using VisualGrid® software (http://www.gpc-biotech.com). Keywords: other

2004-07-03 | GSE1510 | GEO

Transcription profiling of mouse liver to identify hepatic genes differentially expressed in the presence of the maslinic acid in olive oil

Project description:Two olive oils only differing in the presence of maslinic acid were prepared. Using DNA microarrays, hepatic gene expression was analysed in apoE-deficient mice with a C57BL/6J genetic background Experiment Overall Design: The experimental animals were 12, two-month old, female, homozygous apoE KO mice with a C57BL/6J genetic background. Experiment Overall Design: Two study groups were established: a) one received a chow diet (Teklad Mouse/Rat Diet no. 2014, Harlan Teklad, Harlan IbÃ©rica, Barcelona, Spain) supplemented with 10% (w/w) olive oil (diet OO) (n=6), and b) the other received the same chow diet but supplemented with 10% (w/w) maslinic acid- enriched olive oil (diet MAOO; n= 6 and).

2009-01-25 | E-GEOD-7091 | biostudies-arrayexpress

Effect of Oleanolic acid on liver transcriptome of mice lacking apolipoprotein E

Project description:The hypothesis that the oleanolic acid of olive oil might influence hepatic gene expression in an apoE was tested in mice. Gene expression was analyzed using DNA microarrays in male apoE-deficient mice that received 10 mg/kg/day of oleanolic acid for 11 weeks.

2014-03-20 | GSE43589 | GEO

Effect of squalene on liver transcriptome of mice lacking apolipoprotein E

Project description:The hypothesis that the squalene of olive oil might influence hepatic gene expression in an apoE and sex-dependent ways was tested in mice. Gene expression was analyzed using DNA microarrays in male apoE-deficient mice that received 1 g/kg/day of squalene for 10 weeks.

2016-03-30 | GSE36932 | GEO

Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1

Project description:Purpose: The goals of this study were to identify the molecular alterations in the SCA1 inferior olive, and determine whether these changes are found in other affected tissues. Methods: mRNA profiling was conducted in two different SCA1 mouse models (Atxn1 154Q/2Q KI and ATXN1-82Q Tg), in two different affected tisues (inferior olive and cerebellum) during early disease initiation and progression (5 week and 12 week time-points). All analyses were conducted relative to appropriate wild-type controls. TopHat2 v2.1.0 was utilized to align reads to the mouse reference genome (mm10) before quantification and differential expression analysis with Cufflinks v2.2.1. Normalized expression values were generated using Cuffnorm. Results: Differentially regulated genes identified in the SCA1 inferior olive segregated into several enriched biological pathways, including the Defense Response at 12 weeks of age. Our study demonstrates that vulnerable tissues in SCA1 are not uniform in their gene expression changes, and express discrete and commonly enriched biological pathways. In addition, we found that brain region-specific differences occur early in disease initiation and progression at 5 weeks of age. Conclusions: The findings from this study suggest that different mechanisms of neurodegeneration are at work in the SCA1 inferior olive and cerebellum.

2018-12-04 | GSE122099 | GEO

effect of types of olive oil on hepatic gene expression

Project description:Two isocaloric, isonitrogenous diets containing 10% (w/w) olive oil or unsaponifiable-enriched olive oil have been provided to male apo E knockout mice for 11 weeks. Then RNA was isolated and hepatic gene expression analyzed. Keywords: other

2006-02-09 | GSE2261 | GEO

Characterization of the genes that were regulated by feeding with CBM 588

Project description:In the present study, we investigated the effect of CBM 588 on lifespan and multiple-stress resistance using Caenorhabditis elegans as a model animal. When adult C. elegans were fed a standard diet of Escherichia coli OP50 or CBM 588, the lifespan of the animals fed CBM 588 was significantly longer than that of animals fed OP50. Moreover, the worms fed CBM 588 were more resistant to certain stressors, including infections with pathogenic bacteria, UV irradiation, and the metal stressor Cu2+. CBM 588 failed to extend the lifespan of the daf-2/IR, daf-16/FOXO and skn-1/Nrf2 mutants. Transcriptional profiling comparing CBM 588-fed and control-fed animals suggested that DAF-16-dependent class II genes were regulated by CBM 588. In conclusion, CBM 588 extends the lifespan of C. elegans probably through regulation of the insulin/IGF-1 signaling (IIS) pathway and the Nrf2 transcription factor, and CBM 588 improves resistance to several stressors in C. elegans.

2018-12-01 | GSE123163 | GEO

De Novo Design of Adaptive Hydrogels with Solubilized Flavonoids for Whole Layer Regeneration of Diabetic Wound

Project description:A whole layer functional regeneration can be achieved by Gel-Fla, which ensures an improved healing effect than commercial dressing approaches. The multi-level and stereo regeneration Gel-Fla system provides a promising strategy in diabetic wound healing.

2024-03-08 | GSE260761 | GEO

Clostridium butyricum MIYAIRI 588-induced protectin D1 has an anti-inflammatory effect on antibiotic-induced intestinal disorder

Project description:Metabolites are thought as the end products in cellular regulatory processes and their levels show the strongest relationships with the phenotype. Previously, we showed that the administration of Clostridium butyricum MIYAIRI 588 (CBM 588) upregulated protectin D1, an anti-inflammatory lipid metabolite, in colon tissue under antibiotic therapy. However, how CBM 588 induces protectin D1 expression and whether the metabolite has anti-inflammatory effects on antibiotic-induced inflammation are unclear. Therefore, here, we evaluated the effect of CBM 588 on lipid metabolism and protectin D1 in gut protection from antibiotic-induced intestinal disorders. In the CBM 588 treatment group, expression levels of genes encoding lipid receptors related to the conversion of DHA to protectin D1, such as polyunsaturated fatty acid (PUFA) receptors, G-protein coupled receptor 120 (GPR120), and 15-lipoxygenase (LOX), were increased in colon tissue. CD4+ cells producing interleukin (IL)-4, the main component of T helper type 2 (Th2) cells that can activate 15-LOX, also increased in CBM 588-treated groups even after clindamycin co-administration. In addition, similar to CBM 588, exogenously administered protectin D1 reduced inflammatory cytokines, while IL-10 and TGF-β1, works as anti-inflammatory cytokines, were increased. Our data revealed that CBM 588 activated 15-LOX to enhance protectin D1 production by increasing IL-4-producing CD4+ cell population in the intestinal tract. Additionally, CBM 588-induced protectin D1 clearly upregulated IL-10-producing CD4+ cells to control antibiotic-induced gut inflammation. We provide new insights into CBM 588-mediated lipid metabolism induction for the treatment of gut inflammatory diseases.

2020-10-14 | MTBLS2087 | MetaboLights

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