Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

ABSTRACT: Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

PROVIDER: PRJNA837626 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19180491.fastq.gz	Fastqsanger.gz
	SRR19180492.fastq.gz	Fastqsanger.gz
	SRR19180493.fastq.gz	Fastqsanger.gz
	SRR19180494.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

Project description:We applied single-cell RNA-sequencing (scRNA-seq) of vascular endothelial cells isolated from zebrafish embryos at the 24 hours post fertilization (hpf) stage. Six distinct clusters or subclusters related to vascular endothelial cells were identified which include arterial, two venous, cranial, endocardial and endothelial progenitor cell subtypes

2022-05-13 | GSE202912 | GEO

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos.

Project description:Vascular endothelial cells exhibit substantial phenotypic and transcriptional heterogeneity which is established during early embryogenesis. However, the molecular mechanisms involved in establishing endothelial cell diversity are still not well understood. Zebrafish has emerged as an advantageous model to study vascular development. Despite its importance, the single-cell transcriptomic profile of vascular endothelial cells during zebrafish development is still missing. To address this, we applied single-cell RNA-sequencing (scRNA-seq) of vascular endothelial cells isolated from zebrafish embryos at the 24 hpf stage. Six distinct clusters or subclusters related to vascular endothelial cells were identified which include arterial, two venous, cranial, endocardial and endothelial progenitor cell subtypes. Furthermore, we validated our findings by characterizing novel markers for arterial, venous, and endocardial cells. We experimentally confirmed the presence of two transcriptionally different venous cell subtypes, demonstrating heterogeneity among venous endothelial cells at this early developmental stage. This dataset will be a valuable resource for future functional characterization of vascular endothelial cells and interrogation of molecular mechanisms involved in the establishment of their heterogeneity and cell-fate decisions.

| S-EPMC9338088 | biostudies-literature

Single-cell transcriptomic analysis of zebrafish fli1b mutants

Project description:To characterize fli1b role in zebrafish hematopoietic development, we obtained samples from zebrafish fli1b mutant and control wild-type embryos at 23-24 hpf stage. Whole embryo single-cell RNA-seq demonstrated reduction in the expression of hematopoietic markers associated with erythroid and myeloid development. A subset of vascular endothelial markers was also reduced in fli1b mutants. These results demonstrate fli1b role in hematopoietic and vascular development.

2025-03-26 | GSE290550 | GEO

RNAi profiling of zebrafish embryos to investigate regulation of zebrafish endothelial gene expression by miR-126

Project description:Fish, JE, Santoro, MM, Morton, SU, Yu, S, Yeh, RF, Wythe, JD, Ivey, KI, Bruneau, BG, Stainier, DYR, and Srivastava, D. (2008). miR-126 Regulates Angiogenic Signaling and Vascular Integrity. Developmental Cell 15, 272-284. Precise regulation of the formation, maintenance, and remodeling of the vasculature is required for normal development, tissue response to injury, and tumor progression. How specific microRNAs intersect with and modulate angiogenic signaling cascades is unknown. Here, we identified microRNAs that were enriched in endothelial cells derived from mouse embryonic stem (ES) cells and in developing mouse embryos. We found that miR-126 regulated the response of endothelial cells to VEGF. Additionally, knockdown of miR-126 in zebrafish resulted in loss of vascular integrity and hemorrhage during embryonic development. miR-126 functioned in part by directly repressing negative regulators of the VEGF pathway, including the Sprouty-related protein SPRED1 and phosphoinositol-3 kinase regulatory subunit 2 (PIK3R2/p85-Î²). Increased expression of Spred1 or inhibition of VEGF signaling in zebrafish resulted in defects similar to miR-126 knockdown. These findings illustrate that a single miRNA can regulate vascular integrity and angiogenesis, providing a new target for modulating vascular formation and function. Experiment Overall Design: To identify the genes regulated by miR-126 in vivo, flk1:GFP transgenic zebrafish embryos (which express GFP in the endothelium) were injected at the one-cell stage with 4 ng of two independent antisense morpholinos that block the processing of the miR-126 pri-cursor. At 48 hours post-fertilization, endothelial cells were isolated by fluorescence-activated cell sorting from flk1:GFP transgenic fish, and RNA was extracted. Arrays were performed on four biological replicates of control and two independent miR-126 morpholinos.

2008-10-25 | E-GEOD-12012 | biostudies-arrayexpress

Single-cell transcriptomic analysis of 36 hpf Zebrafish etv2 and jam2b positive cells

Project description:We performed single-cell RNAseq analysis of FACs sorted etv2 and jam2b psoitive cells from etv2Gt(2A-Venus) ; jam2bGt(2A-Gal4);UAS:NTR-mCherry zebrafish embryos at 36 hpf using 10x Genomics' Chromium platform. 18 distinct cell populations were identified including vascular endothelial cells and LPM cells.

2021-07-13 | GSE179926 | GEO

The effect of cardiac troponin T2 knockdown on gene expression in zebrafish embryos

Project description:We examined the transcriptional effect of preventing cardiac contraction in zebrafish embryos which can be deprived of circulation without experiencing hypoxia since the fish obtain sufficient oxygen via diffusion. Morpholino antisense knockdown of cardiac troponin T2 (tnnt2) prevented cardiac contraction without affecting vascular development. We concluded that absence of hemodynamic force induces endothelial CXCR4a up-regulation and promotes recovery of blood flow. We used microarrays to define the genetic signatures of the development of collateral vessels in zebrafish. Keywords: Time course comparison of wild type zebrafish embryos and morpholino antisense against troponin t2 treated embryos.

2009-06-24 | GSE16740 | GEO

Single-cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells

Project description:Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock-down embryos.

2021-12-21 | GSE186565 | GEO

Transcription profiling of zebrafish embryos following cardiac troponin T2 knockdown

Project description:We examined the transcriptional effect of preventing cardiac contraction in zebrafish embryos which can be deprived of circulation without experiencing hypoxia since the fish obtain sufficient oxygen via diffusion. Morpholino antisense knockdown of cardiac troponin T2 (tnnt2) prevented cardiac contraction without affecting vascular development. We concluded that absence of hemodynamic force induces endothelial CXCR4a up-regulation and promotes recovery of blood flow. We used microarrays to define the genetic signatures of the development of collateral vessels in zebrafish. Experiment Overall Design: One cell zebrafish embryos were injected with morpholino antisense against control or cardiac troponin t2, which prevents cardiac development. Whole embryo RNA was extracted at 36, 48, and 60h post fertilization and transcriptionally profiled.

2009-07-05 | E-GEOD-16740 | biostudies-arrayexpress

Differentially expressed genes in zebrafish vascular development

Project description:The goal of this experiment was to identify using tissue specific transgenic zebrafish (Fli:EGFP), genes of interest important for embryonic vascular development. Keywords: time course, GFP cell isolation, zebrafish The experiment contained 6 samples. A18, A24 = total RNA isolated from 18 and 24 hpf zebrafish embryo; B2, C and D2=RNA isolated from GFP positive cells sorted at 18, 24 and 28 hpf respectively from Tg(Fli1:EGFP) embryos; E2 = RNA isolated from GFP positive cells sorted at 18 hpf from Tg(Flk:GRCFP) embryos.

2010-05-22 | E-GEOD-12516 | biostudies-arrayexpress

ATACseq of kdrl-GFP+ endothelial cells in 28hpf zebrafish embryos

Project description:ATACseq of kdrl-GFP+ endothelial cells in 28hpf zebrafish embryos

| PRJNA601524 | ENA