Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq facilitates quantitative analysis of wildtype, pdia6 -/- and focad -/- zebrafish livers transcriptome

ABSTRACT: pdia6 knockout zebrafish and focad knockout zebrafish were generated to model liver diseases observed in human patient. Livers were harvested from wt, pdia6 -/- and focad -/- adult zebrafish for RNASeq to study its transcriptome profile.

ORGANISM(S): Danio rerio

PROVIDER: GSE168961 | GEO | 2022/04/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNAseq facilitates quantitative analysis of wildtype, pdia6 -/- and focad -/- zebrafish livers transcriptome

Project description:RNAseq facilitates quantitative analysis of wildtype, pdia6 -/- and focad -/- zebrafish livers transcriptome

| PRJNA714665 | ENA

Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

Project description:The goal of this study is genomic chromatin accessibility of 120 hpf zebrafish livers by ATAC-Seq. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and the DNA methylation profile using reduced representation bisulfite sequencing (RRBS).

2021-07-07 | GSE173792 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype, akr1a1a-/- and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes

Project description:Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors (insra/insrb) expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level, we performed full genome RNA-Seq between akr1a1a+/+, akr1a1a-/- and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA-Seq, including quality control, principal component analysis (PCA), and volcano plots of regulated genes showed comparable properties between akr1a1a mutants, wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down-regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis (normalized enrichment score, -1.888, p=0.028; -1.93, p=0.019). Intriguingly, downstream signaling pathways including MAPK, signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down-regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together, these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore, we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA-seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions.

2021-09-05 | GSE168786 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1-/- Zebrafish Embryo Transcriptomes

Project description:Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level, we performed full genome RNA-Seq between aldh3a1+/+ and aldh3a1-/- larvae at 48 hpf.An overview of RNA-Seq, including quality control, principal component analysis (PCA), volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis (normalized enrichment score, -1.72; p=0.0006). Interestingly, endocrine pancreas but not exocrine pancreas development pathway was significantly down-regulated in aldh3a1 mutants . Taken together, these results further suggest Aldh3a1 as an important regulator in the development, morphology and insulin secretion function of primary pancreas. Furthermore, we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-10-06 | GSE151770 | GEO

DIA-based quantitative proteomic analysis of adult sec31a-nju221 zebrafish liver

Project description:We found that adult zebrafish bearing a homozygous hypomorphic mutation in the sec31a gene (sec31anju221) exhibited overt glycogenic hepatopathy. As an efforts to investigate how hepatic metabolic maladaptation happened in sec31anju221 fish, livers were dissected from the adult zebrafish and DIA-MS was applied.

2024-08-28 | PXD048925 | Pride

RNAseq of livers from WT mice or livers with Rbfox2 knockout fed CD

Project description:RNAseq of livers from WT mice or livers with Rbfox2 knockout fed CD

| PRJNA637086 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of Zebrafish Osteoporosis Model Transcriptomes

Project description:The development of predictive markers to determine the tipping point prior to the onset of osteoporosis is essential to mitigate further irrevocable deterioration. In order to determine the early warning signs before osteoporosis, we used the dynamic network biomarker (DNB) approach to analyze the time series gene expression data in the zebrafish osteoporosis model and revealed that cyclin-dependent kinase inhibitor 1A (cdkn1a) is one core member of DNB. We demonstrated that cdkn1a negatively regulates osteogenesis, evidenced by the loss-of-function and gain-of-function studies. On one hand, CRISPR/Cas9-mediated cdkn1a knockout in the zebrafish significantly altered skeletal development and increased bone mineralization. On the other hand, inducible cdkn1a expression significantly contributed to the osteoclast differentiation. We also provide mechanistic clues that cdkn1a participates in osteoclast differentiation by regulating its upstream signaling cascades. Our data provided new insights into the dynamic nature of osteoporosis, and identified cdkn1a as the early-warning signals of osteoporosis onset.

2023-01-01 | GSE194301 | GEO

RNAseq of regenerating yap mutant zebrafish hearts

Project description:A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration.

2018-10-30 | GSE112452 | GEO

Transcriptomic profiling of Tg(fabp10a:hUHRF1-EGFP)high zebrafish livers and control siblings at 5 dpf

Project description:Overexpression of high levels of human UHRF1 tagged with EGFP (hUHRF1-EGFP)high in zebrafish hepatocytes induces cellular senescence by 5 days post fertilization (dpf) and hepatocellular carcinoma by 15-20 dpf. The goal of this study is to compare the transcriptome profile of zebrafish livers with (hUHRF1-EGFP)high overexpression compared to WT siblings. RNAseq was performed on RNA extracted from pools of microdissected liveres by using RiboZero libary prep to capture all transcripts, including transposable elements, that are expressed in the livers.

2023-03-21 | GSE227735 | GEO

Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

Project description:Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

| PRJNA727017 | ENA