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Lack of hepatic response of microRNA in mice following DB[a,h]A exposure (Agilent miRNA)

ABSTRACT: Dibenzo[a,h]anthracene DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5, and 25 mg/kg/day DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each DB[a,h]A dose tested, and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis revealed minor changes in the mRNA expression for the two lowest doses. Differential expression of 19 up-regulated and 22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25 mg/kg/day DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32 down-regulated (FDR-adjusted P < 0.05 and fold-change > 1.5). Major effect on mRNA expression resulted from exposure to the highest dose (25 mg/kg/day) of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change > 1.5 (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism, glucose metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated miRNA response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold.

ORGANISM(S): Mus musculus

PROVIDER: GSE35195 | GEO | 2013/07/02

SECONDARY ACCESSION(S): PRJNA155965

REPOSITORIES: GEO

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Lack of hepatic response of microRNA in mice following DB[a,h]A exposure (Agilent expression)

Project description:Dibenzo[a,h]anthracene DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5, and 25 mg/kg/day DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each DB[a,h]A dose tested, and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis revealed minor changes in the mRNA expression for the two lowest doses. Differential expression of 19 up-regulated and 22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25 mg/kg/day DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32 down-regulated (FDR-adjusted P < 0.05 and fold-change > 1.5). Major effect on mRNA expression resulted from exposure to the highest dose (25 mg/kg/day) of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change > 1.5 (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism, glucose metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated miRNA response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold.

2013-07-02 | GSE35215 | GEO

Lack of hepatic response of microRNA in mice following DB[a,h]A exposure (Agilent expression)

2013-07-02 | E-GEOD-35215 | biostudies-arrayexpress

Lack of hepatic response of microRNA in mice following DB[a,h]A exposure (Agilent miRNA)

2013-07-02 | E-GEOD-35195 | biostudies-arrayexpress

Effect of LPS and the glucocorticoid dexamethasone on the mouse Bone Marrow Derived Macrophage Proteome

Project description:The concentrations and copy number of proteins in the mouse Bone Marrow Derived proteome was determined for control, 10 ng/mL LPS stimulation, and LPS stimulation plus the addition of 100 nM dexamethasone, after an incubation for 24 hours and with four biological replicates for each condition. Over 6000 proteins were detected, 410 of which were upregulated by LPS (> 1.5-fold increase, adjusted p value < 0.05). 125 of these LPS-induced proteins were significantly regulated by Dexamethason > 1.5 fold 899 increase or decrease, adjusted p value <0.05).

2024-01-26 | PXD041375 | Pride

Expression profiles and bioinformatic analysis of circRNAs in cardiac fibrosis of db/db mice

Project description:To identify the differential expression of circRNAs in cardiac fibrosis of db/db mice, db/db mice cardiac apex tissues were detected through microarray analysis at the age of 21 weeks. Compared with normal control mice, 77 circRNAs were up-regulated and 135 circRNAs were down-regulated in the chromosomes of db/db mice (fold changes ≥1.5, p-values ≤ 0.05). Moreover, Real-time qPCR was performed to validate the expression of circRNAs. In db/db mice, the top four up-regulated circRNAs, mmu_circRNA_28667, mmu_circRNA_32303, mmu_circRNA_20674, mmu_circRNA_25425 were verified. In db/db mice, the top four down-regulated circRNAs which were indexed by circBase database were verified. They were mmu_circRNA_014302, mmu_circRNA_001535, mmu_circRNA_005522 and mmu_circRNA_013422.

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Expression data from the kidney of Sprague-Dawley rats given colistin methanesulfonate sodium

Project description:To investigate the mechanism of nephrotoxicity, colistin methanesulfonate sodium (CMS; 25 or 50 mg/kg) was administered via intraperitoneal injection to Sprague–Dawley rats daily over 7 d. Affymetrix GeneChip microarrays indicated 894 differentially expressed genes in groups treated with CMS (ANOVA, FDR < 0.05, fold change ≥ 1.3).

2018-10-26 | GSE121792 | GEO

Next-Generation Sequencing Identifies Differentially Expressed Genes in Embryonic Hearts Following Caffeine Treatment

Project description:Purpose: This study aimed to identify differentially expressed genes including alternative splice variants in embryonic ventricles following in utero caffeine treatment. Methods: Pregnant CD-1 mice were injected with 20 mg/kg of caffeine or vehicle control daily from embryonic day (E) 6.5-9.5. On E10.5, total RNA was isolated from embryonic ventricles and used for transcriptomic RNA sequencing with Illumina HiSeq 2000 (1X75bp). RNA-seq reads were aligned to the mouse genome (build mm10) with the Tophat for Illumina tool in the PSU galaxy platform. Counting and annotation of RNA-seq reads as well as alternative splicing analysis were performed with Partek Genomics Suite version 6.11. Differential expression of gene and transcript reads between treatments was analyzed with R package EdgeR. Genes/transcripts with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Differentially expressed genes were defined as genes with altered expression at either gene or transcript level. Unique differentially expressed genes were identified by combining the results from annotations with the RefSeq Transcripts (2013-05-10) or Ensembl Transcripts release 71 databases. Results: Differential expression analysis revealed that 59 genes and 451 transcripts were significantly up-regulated, and 65 genes and 398 transcripts were down-regulated by prenatal caffeine treatment (fold change >1.5 or <-1.5; p-value with FDR<0.05). In total, 900 unique genes were identified to have altered expression either at the gene or transcription level. Further analysis with Partek GS revealed that 183 genes had abnormal alternative splicing at the exon level after in utero caffeine treatment. Conclusions: In utero caffeine exposure caused gene expression changes in embryonic ventricles and these changes may lead to long-term effects on cardiac morphology and function.

2015-01-07 | GSE56902 | GEO

Hepatic transcriptomic alterations for 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (TBB) after 5-day exposure in rats

Project description:To identify liver transcripts differentially expressed due to treatment with 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (TBB), we collected RNA from male Harlan Sprague Dawley rats exposed to 0, 0.05, 0.55, 5.50, 55 or 550 mg/kg TBB, 5 days after exposure for animals 7 weeks of age. These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array. A total of 1,0,2,2, and 66 gene transcripts were differentially expressed due to TBB treatment after exposure to 0.05, 0.55, 5.50, 55 or 550 mg/kg TBB (false discovery rate (FDR) < 0.05).

2020-07-15 | GSE153361 | GEO

Hepatic transcriptomic alterations for hexachlorocyclopentadienyl-dibromocyclooctane (HCDBCO) after 5-day exposure in rats

Project description:To identify liver transcripts differentially expressed due to treatment with hexachlorocyclopentadienyl-dibromocyclooctane (HCDBCO), we collected RNA from male Harlan Sprague Dawley rats exposed to 0, 0.05, 0.54, 5.41, 54.1 or 541 mg/kg HCDBCO, 5 days after exposure for animals 7 weeks of age. These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array. A total of 0,0,0,12, and 19 gene transcripts were differentially expressed due to HCDBCO treatment after exposure to 0.05, 0.54, 5.41, 54.1 or 541 mg/kg HCDBCO (false discovery rate (FDR) < 0.05).

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To determine the potential molecular mechanisms by which STAT5 signaling controls colonic crypt homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).

Project description:Reads were aligned to the mm10 genome with annotations provided by Ensembl. Transcripts were filtered, requiring at least 3 reads in 50% of samples within at least one condition. To identify differentially-regulated transcripts, we performed ANOVA (FDR-corrected p<0.05) and required the fold change to exceed 1.5.

2019-04-02 | GSE112607 | GEO

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