Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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).

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Danio rerio

SUBMITTER: Fabian Essfeld

PROVIDER: E-MTAB-14183 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Project description:In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole (CAS 60-56-0), a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole 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 NovaSeq 6000 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-14184 | biostudies-arrayexpress

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

Project description:In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid (CAS 96-83-3), a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 NovaSeq 6000 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-14185 | biostudies-arrayexpress

mRNA-Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups

Project description:In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole, a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee (FRAC) classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System 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 substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.

2024-01-01 | E-MTAB-13269 | biostudies-arrayexpress

mRNA-Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups

Project description:In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl, a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee (FRAC) classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System 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 substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.

2024-01-01 | E-MTAB-13270 | biostudies-arrayexpress

Quantitative proteome fin(ger)prints of triiodthyronin interference with the thyroid system in zebrafish embryos as 3R alternative in environmental hazard assessment

Project description:Endocrine disruption (ED) can trigger far-reaching effects on environmental populations, justifying a refusal of market approval for chemicals with ED properties. For the assessment of ED effects on the thyroid system, regulatory decisions mostly rely on amphibian studies. Here we present a rapid and reproducible data dependent proteomics approach for identifying comprehensive molecular signatures of interference with the thyroid system in zebrafish (Danio rerio) embryos as an alternative to animal testing. For this, we have analysed the thyroid hormone thyronin (T3) as model substances for thyroidal activity in a modified zebrafish embryo toxicity test (zFET). These fingerprints allow for a definition of solid biomarkers as tools in screening approaches and for integration in chronic toxicity studies for suspect substances, such as the fish early life-stage test (OECD TG 210).

2021-01-14 | PXD019111 | Pride

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

Digital Gene Expression (DGE) of thyroid hormone (T3)-responsive genes in C17.2 cells stably transfected with thyroid hormone receptors alpha and beta

Project description:Tagged versions of thyroid hormone receptors alpha (TRa) and beta (TRb) were stably transfected in two C17.2 cell lines, C17.2a and C17.2b, respectively. Cells were treated with 10-7 M T3 for 6, 12 or 24h or left untreated. We performed DGE by sequencing all polyA RNA according to a SAGE-derived method. Differential gene expression after T3 treatment was computed and the T3 responses induced by the two receptors were compared. We could conclude that, in a similar environment, target genes are only partially shared and that a significant proportion show receptor preference and even selectivity. Examination of thyroid hormone target genes over time in two cell lines (C17.2a, C17.2b), each expressing one of the thyroid hormone receptors (alpha, beta).

2012-12-31 | E-GEOD-38539 | 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

2011-10-31 | E-GEOD-32445 | biostudies-arrayexpress

Integrin αvβ3 acting as membrane receptor for thyroid hormones mediates angiogenesis in malignant T cells

Project description:We have found that thyroid hormones (THs), acting as soluble integrin αvβ3 ligands, activate growth-related signaling pathways in T-cell lymphomas (TCL). Specifically, TH-activated αvβ3 integrin signaling promotes TCL proliferation and angiogenesis, in part, via the up-regulation of VEGF. CUTLL1 cells were treated with T3- and T4-bound agarose or agarose alone for 24hrs. Total RNA was harvested from cells and used for expression profiling via RNA-seq.

2015-02-18 | E-GEOD-63122 | biostudies-arrayexpress

Expression data from mouse liver over-expressing either GFP alone or biotinylated-TRb1 and GFP

Project description:We over-expressed biotinylated-thyroid hormone receptor beta 1 (TRb1) in mouse liver using an adenovirus in order to perform ChIP-seq experiments. These microarrays were performed to determine gene expression changes in response to tri-iodothyronine (thyroid hormone; T3) stimulation. A control GFP adenovirus was used and gene expression from these livers was also done as a comparison. We performed microarrays from Ad-GFP-infected propylthiouracil (PTU)-fed livers injected with either saline or T3 and Ad-TRb1-GFP infected livers injected with either saline or T3. RNA was extracted from livers of biotin ligase (BirA)-expressing mice that had been infected with either Ad-GFP or Ad-TRb1, fed with PTU for 3 weeks followed by saline or T3 injections for 4 consecutive days.

2013-12-18 | E-GEOD-52433 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data