Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profile of zebrafish eyes after exposure to 350 mg/L Propylthiouracyl (PTU)

ABSTRACT: Transcriptional profile of zebrafish eyes after exposure to 350 mg/L Propylthiouracyl (PTU)

PROVIDER: PRJNA497083 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional profile of zebrafish eyes after exposure to 350 mg/L Propylthiouracyl (PTU)

Project description:Vertebrate eye devlopment is partially regulated by thyroid hormones. Propylthiouracyl is a pharmaceutical that lowers thyroid hormone levels. We investigated the effects of PTU on eye development of zebrafish. We expected PTU exposure to cause transcriptional changes of visual-system-related genes, which find their phenotypic anchoring in eye malformations and dysfunction, as observed in our previous studies. Additionally, the reversibility of effects after recovery in clean water for three days was investigated.

2019-05-09 | GSE121334 | GEO

Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for 24 hours (collected at 120 hpf)

Project description:Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from 96-120 hours post fertilization (hpf).

2020-06-23 | GSE151291 | GEO

Microarray analysis of eyes only from 23-hpf wild-type and pitx2M64* homozygous mutant zebrafish embryos

Project description:We have developed a pitx2 knockout zebrafish line (c.190_197delATGTCGAC, p.(Met64*)) that recapitulates the characteristic phenotypes of PITX2-mediated Axenfeld-Rieger syndrome (ARS) as well as displays some unique ocular phenotypes that in humans have implicated possible PITX2 involvement.To begin to ascertain the downstream pathways that are disrupted in pitx2M64* homozygous mutants, RNA from 23-hpf wild-type and pitx2M64* homozygous eyes only was submitted for microarray analysis.To collect embryonic ocular tissues from mutant and wild-type embryos, whole eyes of 23-hpf embryos were dissected; wild-type and pitx2M64* homozygous mutant whole eyes were then pooled together respectively for RNA extractions. RNA was extracted from the collected eyes using TRIzol, assessed for quality and assigned RNA Integrity Numbers (RINs), and submitted as three independent collections each to OakLabs (Hennigsdorf, Germany) for transcriptome and statistical analysis.

2018-03-13 | E-MTAB-6463 | biostudies-arrayexpress

A comparison of the gene expression between the lens and body without eyes of larval zebrafish

Project description:The lens of the eye is consisted of lens fiber cells that undergo large-scale organelle degradation during terminal differentiation. To understand the molecular mechanism of large-scale organelle degradation, we compared the gene expression profiles between the lens and body without eyes of larval zebrafish using a microarray analysis.

2021-04-20 | GSE168029 | GEO

Transcriptional profile of zebrafish eyes after exposure to 200 ug/L Tetrabromobisphenol A (TBBPA)

Project description:Transcriptional profile of zebrafish eyes after exposure to 200 ug/L Tetrabromobisphenol A (TBBPA)

| PRJNA497088 | ENA

RNA-Seq analysis of Wild Type and lrpap1-/- zebrafish eyes at three month

Project description:Zebrafish is a good model organism for studying eye diseases, but there is a lack of transcriptome information, especially as it related to myopia. The aim of this study was to compare transcriptome differences between lrpap1-/- mutant and wild-type zebrafish eyeballs. Eye tissue mRNA profiles of three-month-old wild-type (WT) and low-density lipoprotein receptor-related protein-associated protein 1 knockout (lrpap1-/-) zebrafishes were generated by deep sequencing using Illumina HiSeq2500. RNA-seq reads were aligned to the zebrafish genome(Ensembl, GRCz11) using HISAT2, TPM was used to further normalize gene expression counts between all samples. Differentially expressed genes (DEG) were determined by DESeq2, which was based on the Negative Binomial Generalize Linear Model. Finally, there are 1661 differentially expressed genes between the mutant and the wild-type zebrafish eyeballs using the criterion of p-value <0.05 and ׀Log (Fold Change)|>1 ,among which 1209 genes are up-regulated, and 452 genes are down-regulated in the mutants. Our study shows the first detailed analysis of zebrafish eyes transcriptomes by RNA-seq technology. The transcriptome information provided in this study may help to reveal the molecular mechanism of genetic myopia.

2021-11-02 | GSE186889 | GEO

Sinorhizobium medicae strain:350

Project description:Sinorhizobium medicae 350 Resequencing

| PRJNA499394 | ENA

Elevated MG-H1 in glo1-/-aldh3a1-/- zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity

Project description:Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites, leading to increased modification of proteins, DNA and lipids, thereby contributing to cellular and tissue dysfunction in diabetes, diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels, yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels, which partially act as compensatory mechanism. Excess 4-HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae, inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature, glo1-/-aldh3a1-/- zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations, glucose homeostasis, transcriptome, and metabolomics in Tg(fli1:EGFP) zebrafish. glo1-/-aldh3a1-/- zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG-H1 and decreased proteasomal chymotrypsin-like activity, which could be rescued by the MG-H1 scavenger L-carnosine and proteasome activator Betulinic acid treatments. In adult glo1-/-aldh3a1-/- zebrafish, impaired glucose metabolism, angiogenic retina vasculature and thickened GBM were observed. Thus, our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG-H1, possibly through reduced proteasome activity.

2024-07-01 | GSE270442 | GEO

Bradyrhizobium diazoefficiens strain:USDA 350 | isolate:USDA 350

Project description:Bradyrhizobium diazoefficiens USDA 350 genome sequencing

| PRJNA1143003 | ENA

High-throughput sequencing analysis identify miRNAs in 7dpf F1-zebrafish under Î²-diketone antibiotics exposure to F0-zebrafish

Project description:Small RNA high-throughput sequencing technology was used to characterize the miRNAs in F1-zebrafish after 90-day Î²-diketoneÂ antibiotic (DKA) exposure to F0-zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7-dpf F1-zebrafish were constructed. In total, 10,117,347, 9,818,830 and 12,049,949 raw reads were acquired, respectively, under the different DKA-exposure treatments (0, 6.25 mg/L and 12.5mg/L) from the three miRNAs libraries by Illumina sequencing. Low-quality reads were removed, which included 5' contaminants, those missing the 3' primer or insert tag, sequences with a poly A tail, and those shorter than 17 nt and longer than 25 nt. As a result, 8,141,146 (representing 312,735 unique sequences; control), 8,687,210 (representing 251,508 unique sequences; 6.25 mg/L), and 10,569,566 (representing 441,938 unique sequences; 12.5 mg/L) valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar, and the unique sRNA reads were mainly distributed in the 20-24 nt range, among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads, respectively. The 22-nt sRNAs were the most abundant, with the length distribution of counts of sequ-seqs and unique miRNAs displaying a normal distribution. Sample 1: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 12.5 mg/L.

2016-07-30 | E-GEOD-85004 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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