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RNA-Seq of zebrafish embryos (96hpf) treated with different concentrations of Triiodothyronine (T3) below acute toxicity levels against untreated control groups

ABSTRACT: RNA-Seq of zebrafish embryos (96hpf) treated with different concentrations of Triiodothyronine (T3) below acute toxicity levels against untreated control groups

PROVIDER: PRJEB38271 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4140030.fastq.gz	Fastqsanger.gz
	ERR4140031.fastq.gz	Fastqsanger.gz
	ERR4140032.fastq.gz	Fastqsanger.gz
	ERR4140033.fastq.gz	Fastqsanger.gz
	ERR4140034.fastq.gz	Fastqsanger.gz

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RNA-Seq of zebrafish embryos (96hpf) treated with different concentrations of Triiodothyronine (T3) below acute toxicity levels against untreated control groups

Project description:The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish (Danio rerio) embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine (T3, CAS: 6893-02-3) was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE), high exposure (HE) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.

2020-09-30 | E-MTAB-9056 | biostudies-arrayexpress

RNA-Seq of zebrafish embryos (96hpf) treated with different concentrations of Triiodothyronine (T3) against untreated control groups

Project description:RNA-Seq of zebrafish embryos (96hpf) treated with different concentrations of Triiodothyronine (T3) against untreated control groups

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RNA-Seq of zebrafish embryos (96hpf) treated with different concentrations of Triiodothyronine (T3) against untreated control groups

Project description:In the present study transcriptome analysis was employed to investigate the early molecular responses to T3 (3, 3′,5-Triiodo-L-thyronine, CAS 6893-02-3), thyroid hormone receptor agonist. Zebrafish embryos were exposed to T3 according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 system (Illumina Inc., San Diego, USA) and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes (DEGs).

2024-09-01 | E-MTAB-14183 | biostudies-arrayexpress

Identical gene regulation patterns of triiodothyronine (T3) and selective thyroid hormone receptor modulator GC-1

Project description:This SuperSeries is composed of the following subset Series: GSE32443: Identical gene regulation patterns of triiodothyronine (T3) and selective thyroid hormone receptor modulator GC-1 [Affymetrix] GSE32444: Identical gene regulation patterns of triiodothyronine (T3) and selective thyroid hormone receptor modulator GC-1 [Illumina] Refer to individual Series

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Rewiring of liver diurnal transcriptome rhythms by triiodothyronine (T3) supplementation

Project description:Diurnal (i.e., 24-hour) physiological rhythms depend on transcriptional programs controlled by a set of circadian clock genes/proteins. Systemic factors like humoral and neuronal signals, oscillations in body temperature, and food intake align physiological circadian rhythms with external time. Thyroid hormones (THs) are major regulators of circadian clock target processes such as energy metabolism, but little is known about how fluctuations in TH levels affect the circadian coordination of tissue physiology. In this study, a high triiodothyronine (T3) state was induced in mice by supplementing T3 in the drinking water, which affected body temperature, and oxygen consumption in a time-of-day dependent manner. 24-hour transcriptome profiling of liver tissue identified 37 robustly and time independently T3 associated transcripts as potential TH state markers in the liver. Such genes participated in xenobiotic transport, lipid and xenobiotic metabolism. We also identified 10 – 15 % of the liver transcriptome as rhythmic in control and T3 groups, but only 4 % of the liver transcriptome (1,033 genes) were rhythmic across both conditions – amongst these several core clock genes. In-depth rhythm analyses showed that most changes in transcript rhythms were related to mesor (50%), followed by amplitude (10%), and phase (10%). Gene set enrichment analysis revealed TH state dependent reorganization of metabolic processes such as lipid and glucose metabolism. At high T3 levels, we observed weakening or loss of rhythmicity for transcripts associated with glucose and fatty acid metabolism, suggesting increased hepatic energy turnover. In sum, we provide evidence that tonic changes in T3 levels restructure the diurnal liver metabolic transcriptome independent of local molecular circadian clocks.

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Rewiring of liver diurnal transcriptome rhythms by triiodothyronine (T3) supplementation

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mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Imidacloprid below acute toxicity levels against untreated control groups

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mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups

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mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Carbaryl below acute toxicity levels against untreated control groups

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