Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Zebrafish control and csf1r mutant microglia and brain transcriptomes

ABSTRACT: Zebrafish control and csf1r mutant microglia and brain transcriptomes

PROVIDER: PRJNA477787 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7419820.fastq.gz	Fastqsanger.gz
	SRR7419830.fastq.gz	Fastqsanger.gz
	SRR7419840.fastq.gz	Fastqsanger.gz
	SRR7419850.fastq.gz	Fastqsanger.gz
	SRR7419860.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 78

Similar Datasets

Zebrafish control and csf1r mutant microglia transcriptomes

Project description:Purpose: Identify zebrafish control and csf1r-mutant microglia transcriptomes Methods: RNA sequencing was performed on FACS-sorted control microglia (3x), csf1ra-/- microglia (3x) and csf1ra-/-;b+/- microglia (3x). 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10. Results: We identified that csf1ra-/- or csf1ra-/-;b+/- microglia transcriptomes retain most of the microglia gene expression signature but mostly show changes in chemoklines expression.

2018-07-20 | GSE116215 | GEO

Zebrafish control and csf1r mutant brain transcriptomes

Project description:Purpose: Identify zebrafish control and csf1r-mutant brain transcriptomes Methods: RNA sequencing was performed on whole brain of control (3x), csf1ra-/- microglia (3x) and csf1ra-/-;b+/- microglia (3x) and csf1ra-/-;b-/- zebrafish. 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10. Results: We identified that microglia gene expression was reduced in csf1ra-/-;b+/- and csf1ra-/-;b-/;- mutant transcriptomes.

2018-07-20 | GSE116216 | GEO

Zebrafish control and csf1r mutant microglia transcriptomes

Project description:Zebrafish control and csf1r mutant microglia transcriptomes

| PRJNA477793 | ENA

Zebrafish control and csf1r mutant brain transcriptomes

Project description:Zebrafish control and csf1r mutant brain transcriptomes

| PRJNA477792 | ENA

Differential CSF1R signaling enables widespread integration of genetically unmodified human microglia into the mouse brain

Project description:Microglia are long-lived myeloid cells in the central nervous system that are implicated in many neurological diseases. The differentiation of pluripotent stem cells provides an opportunity to develop in vitro human cellular models carrying disease gene mutations complementing existing animal models of disease. Microglia are particularly sensitive to their cellular environment and can adopt a variety of reactive states depending on different pathological conditions which may be difficult to mimic in vitro. Therefore, to best investigate human microglia in vivo, it would be helpful to generate mice whose endogenous microglia are exchanged with human cells without the need of genetic manipulation of donor cells which could alter microglia function. Colony stimulating factor 1 receptor (CSF1R) signaling is critical for microglial survival in mice, and humans with CSF1R mutations are born with fewer microglia. We made the surprising discovery that transplanted human pluripotent stem cell-derived microglia (hMG) survive pharmacological CSF1R inhibition unlike endogenous mouse microglia. Cellular assays confirmed that CSF1R signaling is necessary for human microglia survival and revealed differential CSF1R signaling with species-specific ligands. Moreover, receptor ligands and small molecule inhibitors acted in a competitive fashion. Based on these insights, we found that transient CSF1R inhibition after cell transplantation led to near-complete and wide-spread repopulation of hMGs into the mouse brain of immunodeficient mice with humanized CSF1 ligand. This approach allows the facile generation of mice whose brain microglia are replaced with genetically unmodified human cells.

2024-04-11 | GSE263618 | GEO

Zebrafish microglia transcriptome

Project description:Purpose: Identify zebrafish microglia transcriptome in the healthy and neurodegenerative brain. Methods: RNA sequencing was performed on FACS-sorted microglia (3x), other brain cells (3x) and activated microglia (4x). Microglia activation was induced using nitroreductase-mediated cell ablation. 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10. Results: We identified the zebrafish microglia transcriptome, which shows overlap with previously identified mouse microglia transcriptomes. Transcriptomes obtained 24h and 48h after treatment appeared highly similar. Therefore, these datasets were pooled. Additionally, we identified an acute proliferative response of microglia to induced neuronal cell death.

2016-10-20 | GSE86921 | GEO

single-cell RNA-seq profile of microglia under acute Csf1r inhibition and early repopulation in adult brain

Project description:Microglia are the resident myeloid cell in the central nervous system (CNS). Like other terminally differentiated myeloid cells, microglia rely on Csf1r signaling for survival and maintenance. Surprisingly, a small subset of microglia in the murine brain can survive without Csf1r signaling, as shown in Csf1r KO mice as well as in mice that have been treated with Csf1r inhibitor PLX5622. The nature of such Csf1r independent microglial population has not been fully characterized. Here we applied single-cell RNA-seq to examine the remaining microglia in C57/BL6J mice that were treated with PLX5622 diet (1200 mg/kg, 14 days), which results >90% microglial removal.

2020-05-09 | GSE150169 | GEO

Zebrafish control and csf1r mutant microglia and brain transcriptomes

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-07-20 | GSE116217 | GEO

single-cell RNA-seq profile of adult microglia under acute Csf1r inhibition and early repopulation

2019-12-01 | GSE133773 | GEO

RNA-seq of mouse brain tissue investigating the effect of absence of microglia in the developing brain

Project description:Microglia, brain-resident macrophages, have been proposed to play an active role in synaptic refinement and maturation, influencing plasticity and circuit-level connectivity. Using a genetically modified mouse which lacks microglia (Csf1r ∆FIRE/∆FIRE), we investigate the effect on gene expression of the presence or absence of microglia in the developing mouse brain.

2024-08-19 | E-MTAB-14156 | 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