Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of endothelial specific inhibition of Brg1 on gene expression during zebrafish heart regeneration [RNA-seq]

ABSTRACT: To decipher the molecular action of endothelial Brg1 in the regulation of zebrafish heart regeneration, we applied Tg(kdrl:eGFP) to label cardiac endothelial cells including the endocardium, and achieved endothelium-specific over-expression of DN-xBrg1 by using the compound zebrafish line consisting of Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (defined as DNK), while we used Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl-eGFP) as control (CtrlK) in the presence of 4-HT starting at 3 days before ventricular resection. The kdrl:eGFP endothelial cells, which were sorted by FACS (fluorescence-activated cell sorting) from CtrlK and DNK hearts at 7 dpa, were subjected to RNA-seq analysis.

ORGANISM(S): Danio rerio

PROVIDER: GSE200936 | GEO | 2023/04/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Endothelial Brg1-Notch Signaling Regulates Zebrafish Heart Regeneration

Project description:The goal of this study is to compare the NGS-derived heart transcriptome profiling (RNA-seq) between kdrl GFP positive endothelial cells of 4-HT induced Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (DNK) and Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:eGFP) (CtrlK) injured hearts.

2022-07-09 | GSE154193 | GEO

Effect of endothelial specific inhibition of Brg1 on histone marker H3K4me3 in the zebrafish genome [ChIP-seq]

Project description:To decipher the effect of endothelial specific inhibition of Brg1 on histone marker H3K4me3 in the zebrafish genome during zebrafish heart regeneration, we achieved endothelium-specific over-expression of DN-xBrg1 by using the compound zebrafish line consisting of Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl:CreER) (defined as DN), while we used Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1) as control (Ctrl) in the presence of 4-HT starting at 3 days before ventricular resection. The whole ventricles from CtrlK and DNK hearts at 7 dpa were subjected to ChIP-seq analysis using H3K4me3 antibody.

2023-04-03 | GSE200937 | GEO

Transcriptomic profile of zebrafish liver cells in thioacetamide (TAA) model

Project description:Zebrafish transgenic lines Tg(fabp10a:dsRed), Tg(hand2:EGFP) and Tg(kdrl:ras-mCherry) in AB wild-type background were anesthetized with MS-222 and adult females were injected intraperitoneally with 500 mg/kg thioacetamide (TAA) or sterile water as a control 6 times over the course of 2 weeks. We have characterized transcriptomic profiles of FACS-isolated hepatocytes (dsRed+), stellate cells (EGFP+) and liver endothelial cells (mCherry+) from fishes treated with TAA or sterile water. Cells negative for the fluorescence were used as a control.

2021-12-23 | GSE145564 | GEO

Genome-wide chromatin accessibility profiles of zebrafish liver cells in thioacetamide (TAA) model

Project description:Zebrafish transgenic lines Tg(fabp10a:dsRed), Tg(hand2:EGFP) and Tg(kdrl:ras-mCherry) in AB wild-type background were anesthetized with MS-222 and adult females were injected intraperitoneally with 500 mg/kg thioacetamide (TAA) or sterile water as a control 6 times over the course of 2 weeks. We have characterized chromatin accessibility profiles of FACS-isolated hepatocytes (dsRed+), stellate cells (EGFP+) and liver endothelial cells (mCherry+) from fishes treated with TAA or sterile water. Cells negative for the fluorescence were used as a control.

2021-12-23 | GSE145563 | GEO

kdrl:eGFP+ ECs isolated from wildtype, etsrp-null, npas4l-null, and sox32-null zebrafish embryos

Project description:Microarray analysis of triplicate RNA samples isolated from kdrl:eGFP-sorted ECs of wildtype, npas4l-/-, etsrp-/-, and sox32-/- zebrafish embryos in Tg(kdrl:EGFP) transgenic background between 18 and 18.5 hpf.

2020-10-20 | E-MTAB-9698 | biostudies-arrayexpress

A Novel Perivascular Cell Population in the Zebrafish Brain

Project description:Purpose: RNA-seq analysis from isolated zebrafish fluorescent granular perithelial (FGP) cells in adult brains compared to endothelial cells or entire fish. Method: FGPs and endothelium were isolated by FACS sorting using transgenic line Tg(kdrl:mCherry);Tg(mrc1a:eGFP).

2017-05-15 | GSE97421 | GEO

RNAseq analysis of thymic CD4-CD8- double-negative (DN) invariant NKT cells from CD4+CD8+ double-positive (DP)-specific Rag2-conditional knock-out mice

Project description:We report the identification of DN NKT cells developed from DN stage thymocytes. We analyzed the gene expression profiles of NKT cells that have developed from DN stage thymocytes isolated from DP-specific E8III-Cre transgenic Rag2-floxed mouse strain, and NKT cells developed from DP thymocytes sorted as YFP-reporter positive NKT cells that were isolated from E8III-Cre transgenic Rosa26-loxP-STOP-loxP mouse.

2016-11-30 | GSE89532 | GEO

Single-cell transcriptional analysis reveals innate lymphoid cell (ILC)-like cells in zebrafish

Project description:Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tg(cd4-1:mCherry), Tg(lck:EGFP), Tg(mhc2dab:GFP, cd45:dsRed), AB.

2018-11-16 | E-MTAB-7117 | biostudies-arrayexpress

Genome Editing with Tyrosinase gRNA

Project description:We confirmed Tyrosinase genome insertions or deletions of the three Tg mice by deep sequencing using MiSeq. These mice generated gene editing mice by using Tol2 transposon to introduce tyrosinase guide RNA (gRNA) into fertilized eggs obtained by crossing LSL (loxP-stop-loxP)-Cas9 mice with CAG-CreER mice.

2023-02-27 | GSE225711 | GEO

Zebrafish (Danio rerio) Schwann cell, oligodendrocyte lineage, and neuron RNA-sequencing

Project description:RNA-sequencing of cells collected from 72 hpf embryos: Schwann cells (Gt(foxd3:mCherry);Tg(sox10:mEGFP)), oligodendrocyte lineage cells (Tg(olig2:dsred);Tg(sox10:megfp)), and neurons (Tg(nbt:dsred))

2021-05-15 | GSE174486 | GEO

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