Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell transcriptomics on zebrafish gliovascular niche

ABSTRACT: To investigate the cell types involved in the gliovascular niche of the zebrafish brain, we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.

ORGANISM(S): Danio rerio

PROVIDER: GSE225721 | GEO | 2024/04/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single cell transcriptomics on zebrafish gliovascular niche

Project description:Single cell transcriptomics on zebrafish gliovascular niche

| PRJNA937226 | ENA

Gene expression analysis of hematopoietic niche cells in the zebrafish kidney

Project description:The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover, transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney, termed the "kidney marrow", providing an attractive tool for studying hematopoietic niches. Here, we isolated two candidate niche cell populations from the zebrafish kidney, pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low-density lipoprotein (Ac-LDL), whereas pericytes can be labeled by pdgfrb expression. Therefore, pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488-conjugated Ac-LDL, respectively. In addition, we also utilized a cell line generated from the zebrafish kidney, zebrafish kidney stromal (ZKS), which have been shown to support proliferation of various hematopoietic precursors (Stachula et al., 2009). In this study, we performed RNA-seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ (DP) hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells (DP_uncul), gata2a+ runx1+ cells co-cultured with ZKS cells (DP_cocul), and gata2a+ runx1+ cells co-cultured with ZKS cells in the presence of both IWR-1-endo and Thpo (DP_IW+Th).

2022-10-21 | GSE186298 | GEO

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

The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes developmental defects in zebrafish embryos

Project description:The fusion oncoprotein EWS-FLI1 arises from a t(11;22)(q24;q12) chromosomal translocation and causes Ewing's Sarcoma, a malignant bone tumor. The mechanism whereby EWS-FLI1 transforms cells is unknown. We made germline transgenic zebrafish expressing human EWS-FLI1 under the control of the heat shock promoter. Induction of EWS-FLI1 expression causes multiple defects in embryonic development. We compared gene expression in control and transgenic EWS-FLI1 zebrafish. The results identify a conserved set of EWS-FLI1-regulated genes, and provide insight into the pathogenesis of Ewing's Sarcoma tumors. We performed heat shock and isolated total RNA for microarray studies comparing wildtype AB strain zebrafish with transgenic zebrafish expressing human EWS-FLI1 [Tg(HSP:EWS-FLI1)]. RNA was biotin-lableled and hybridized to zebrafish-specific Affymetrix arrays.

2011-11-01 | E-GEOD-31185 | biostudies-arrayexpress

The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes Ewing's-type tumors in zebrafish

Project description:The fusion oncoprotein EWS-FLI1 arises from a t(11;22)(q24;q12) chromosomal translocation and causes Ewing's Sarcoma, a malignant bone tumor. The mechanism whereby EWS-FLI1 transforms cells is unknown. Somatic, mosaic expression of human EWS-FLI1 in zebrafish from the heat shock promoter [Tg(HSP:EWS-FLI1)] caused small round blue cell tumors (SRBCTs) similar to human Ewing's sarcoma. We performed microarray studies comparing zebrafish SRBCTs to another tumor type, zebrafish malignant peripheral nerve sheath tumors (MPNSTs). The results identify a conserved set of EWS-FLI1-regulated genes,and provide insight into the pathogenesis of Ewing's Sarcoma tumors. Zebrafish SRBCTs arising from somatic insertions of the EWS-FLI1 transgene were collected. MPNSTs from non-transgenic fish of the same genetic background were collected in parallel. RNA was prepared from all samples and hybridized to zebrafish-specific Affymetrix arrays.

2011-11-01 | E-GEOD-31186 | biostudies-arrayexpress

Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration

Project description:Regenerating zebrafish fins have distal progenitor and proximal re-differentiation zones. A Wnt-producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration.

2019-12-01 | GSE125859 | GEO

The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes Ewing's-type tumors in zebrafish

Project description:The fusion oncoprotein EWS-FLI1 arises from a t(11;22)(q24;q12) chromosomal translocation and causes Ewing's Sarcoma, a malignant bone tumor. The mechanism whereby EWS-FLI1 transforms cells is unknown. Somatic, mosaic expression of human EWS-FLI1 in zebrafish from the heat shock promoter [Tg(HSP:EWS-FLI1)] caused small round blue cell tumors (SRBCTs) similar to human Ewing's sarcoma. We performed microarray studies comparing zebrafish SRBCTs to another tumor type, zebrafish malignant peripheral nerve sheath tumors (MPNSTs). The results identify a conserved set of EWS-FLI1-regulated genes,and provide insight into the pathogenesis of Ewing's Sarcoma tumors.

2011-11-01 | GSE31186 | GEO

The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes developmental defects in zebrafish embryos

2011-11-01 | GSE31185 | GEO

A zebrafish transgenic model of Ewing's Sarcoma reveals conserved mediators of EWS-FLI1 tumorigenesis

Project description:This SuperSeries is composed of the following subset Series: GSE31185: The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes developmental defects in zebrafish embryos GSE31186: The human Ewing's Sarcoma oncoprotein EWS-FLI1 causes Ewing's-type tumors in zebrafish Refer to individual Series

2011-11-01 | E-GEOD-31217 | biostudies-arrayexpress

Identification of Strip1-interacting partners in zebrafish head proteome

Project description:Zebrafish embryos expressing GFP-tagged wild type form of Strip1 were used for this study, embryos carrying the GFP-tagged mutant form of Strip1 or GFP only were used as negative controls. Co-immunoprecipitation was performed on 2 dpf head lysates using GFP-trap beads. Samples were prepared for mass spectrometry analysis using trypsin based on-bead digestion protocol.

2022-03-16 | PXD028131 | JPOST Repository

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