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RNA-sequencing of liver tissue from corn oil and TCDD treated Fmo3+/+ and Fmo3-/- mice

ABSTRACT: RNA-sequencing of liver tissue from corn oil and TCDD treated Fmo3+/+ and Fmo3-/- mice

PROVIDER: PRJNA789851 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17262570_1.fastq.gz	Fastqsanger.gz
	SRR17262570_2.fastq.gz	Fastqsanger.gz
	SRR17262571_1.fastq.gz	Fastqsanger.gz
	SRR17262571_2.fastq.gz	Fastqsanger.gz
	SRR17262572_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing of liver tissue from corn oil and TCDD treated Fmo3+/+ and Fmo3-/- mice

Project description:Purpose: The goals of this study are to compare the hepatic transcriptome profiles of Fmo3+/+ and -/- mice injected weekly with either corn oil vehicle or 25ug/kg TCDD for 6 weeks data analysis. Methods: RNA was isolated from frozen liver tissue. RNA-Seq libraries were generated using the Illumina mRNA TruSEQ Directional library kit and sequenced using an Illumina NovaSeq 6000 (both according to the manufacturer’s instructions). RNA-Seq was performed by the University of Chicago Genomics Facility. Conclusions: Our study represents the first report of the role of Fmo3 in response to TCDD and finds that genes associated with the acute phase response and detoxification are significantly altered in the absence of Fmo3.

2022-04-27 | GSE191138 | GEO

Transcription profiling of mouse liver from wild-type or genetically deleted AHRs were treated with corn oil vehicle or TCDD reveals aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries

Project description:Conventional biochemical and molecular techniques identified previously several genes whose expression is regulated by the aryl hydrocarbon receptor (AHR). We sought to map the complete spectrum of AHR-dependent genes in male adult liver using expression arrays to contrast mRNA profiles in Ahr-null mice (Ahrâ/â) with those in mice with wild-type AHR (Ahr+/+). Transcript profiles were determined both in untreated mice and in mice treated 19 h earlier with 1000 Âµg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Expression of 456 ProbeSets was significantly altered by TCDD in an AHR-dependent manner, including members of the classic AHRE-I gene battery, such as Cyp1a1, Cyp1a2, Cyp1b1, and Nqo1. In the absence of exogenous ligand, AHR status alone affected expression of 392 ProbeSets, suggesting that the AHR has multiple functions in normal physiology. In Ahrâ/â mice, only 32 ProbeSets exhibited responses to TCDD, indicating that the AHR is required for virtually all transcriptional responses to dioxin exposure in liver. The flavin-containing monooxygenases, Fmo2 and Fmo3, considered previously to be uninducible, were highly induced by TCDD in an AHR-dependent manner. The estrogen receptor alpha as well as two estrogen-receptor-related genes (alpha and gamma) exhibit AHR-dependent expression, thereby extending cross-talk opportunities between the intensively studied AHR and estrogen receptor pathways. p53 binding sites are over-represented in genes down-regulated by TCDD, suggesting that TCDD inhibits p53 transcriptional activity. Overall, our study identifies a wide range of genes that depend on the AHR, either for constitutive expression or for response to TCDD. Experiment Overall Design: Mice bearing wild-type or genetically deleted AHRs were treated with corn oil vehicle or TCDD, and their livers analyzed by expression arrays.

2008-11-13 | E-GEOD-10082 | biostudies-arrayexpress

Fetal mouse heart, TCDD dose-response series

Project description:Pregnant C57Bl6N mice were treated with 0 (corn oil), 1.5, 3.0, or 6.0 ug/kg TCDD on gd14.5. Fetal hearts were collected on gd17.5. Hearts from each litter were pooled onto one chip. 4 replicates of each condition were run on affymetrix MG_U74Av2 chips, using standard affymetrix protocols and controls. Keywords: dose-response, 3 doses plus corn oil control, 4 replicates

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Project description:The purpose of this study was to explore the mechanism of aerobic decay of whole-plant corn silage and the effect of Neolamarckia cadamba essential oil on aerobic stability of whole-plant corn silage. Firstly, the dynamic changes of temperature, microbial community and metabolite content after aerobic exposure of whole-plant corn silage were determined, and the main microbial species and mechanism leading to aerobic spoilage of whole-plant corn silage were analyzed. The N. cadamba essential oil was extracted from fresh N. cadamba leaves by steam distillation, and the minimal inhibitory concentration, antibacterial stability and bacteriostatic mechanism of N. cadamba essential oil against undesirable microorganisms in whole-plant corn silage were determined. According to the minimum inhibitory concentration of N. cadamba essential oil on undesirable microorganisms in silage, N. cadamba essential oil was added to whole-plant corn silage to explore the effect of N. cadamba essential oil on the aerobic stability of whole-plant corn silage.

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Project description:Experiment to study TCDD-elicited effects on metabolite levels in liver of male mice treated with sesame oil vehicle or 0.01-30 ug/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)every 4 days for 28 days using untargeted metabolomics.

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NanoString analysis of a rat liver mRNA panel following TCDD treatment

Project description:Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we fill that gap by comparing two key medium-throughput platforms M-bM-^@M-^S NanoStringM-bM-^@M-^Ys nCounter Analysis System and ABIM-bM-^@M-^Ys OpenArray System M-bM-^@M-^S to gold-standard quantitative real-time RT-PCR. TCDD-sensitive (Long-Evans) and TCDD-resistant (Han/Wistar) rats were used in both time-course and dose response studies to asses the transcriptomic response to TCDD-insult. The time-course experiment saw animals recieve a single dose of 100ug/kg TCDD or corn oil vehicle followed by euthanasia and tissue collection at various time-points. Animals in the dose-response experiment recieved a single dose of TCDD at varying concentrations or corn oil vehicle, followed by euthanasia and tissue collection 19 hours post-treatment. Each treatment group contained 4-5 biologicial replicates.

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