Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptome profiles of wild-type and IRF8KO microglia

ABSTRACT: Single-cell transcriptome profiles of wild-type and IRF8KO microglia

PROVIDER: PRJNA1107159 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28876229_1.fastq.gz	Fastqsanger.gz
	SRR28876229_2.fastq.gz	Fastqsanger.gz
	SRR28876230_1.fastq.gz	Fastqsanger.gz
	SRR28876230_2.fastq.gz	Fastqsanger.gz
	SRR28876231_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Transcriptome profiles of wild-type, IRF8KO microglia

Project description:Transcriptome profiles of wild-type, IRF8KO microglia

| PRJNA1107154 | ENA

Transcriptome profiles of wild-type, IRF8KO microglia

Project description:The lineage-determining transcription factor IRF8's function in microglia is unclear. Our study aims to shed light on this by analyzing the genome-wide, temporal transcriptome profiles of wild-type and IRF8KO microglia. We used deep-sequencing and differential analysis to identify the effects of IRF8 on transcription programs in microglia, such as microglia identity gene expression. This study provides a new understanding of the transcriptional programs in microglia.

2024-07-01 | GSE266422 | GEO

Transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia [RNA-seq]

Project description:The role of the lineage-determining transcription factor IRF8 in microglia remains unelucidated. We report the genome-wide, transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia. Deep-sequencing and subsequent differential analysis revealed the impacts of IRF8 on microglia-specific transcription programs, such as cell identity. Sall1 and Batf3 genes were identified as a downstream transcription factor of IRF8, and Batf3 dependent genes showed correlation with IRF8-dependent genes in microglia. The conditional depletion of IRF8 gene after microglial maturation (P14) increased or decreased the gene expression, most of which were shared with those of IRF8KO. This study provides a novel insight into understanding transcriptional programs in microglia.

2023-06-01 | GSE231403 | GEO

Single-cell transcriptome profiles of wild-type and IRF8KO microglia [scRNA-seq]

Project description:The role of the lineage-determining transcription factor IRF8 in microglia remains unelucidated. We analyzed the transcriptome diversity of wild-type and IRF8KO microglia. Deep-sequencing and subsequent differential analysis revealed the significance of the IRF8-dependent transcription on microglial heterogeneity and self-renewing. This study provides a novel insight into understanding IRF8-mediated transcriptional programs in microglia.

2023-06-01 | GSE231405 | GEO

Transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia [RNA-seq]

Project description:Transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia [RNA-seq]

| PRJNA964778 | ENA

Single-cell transcriptome profiles of wild-type and IRF8KO microglia [scRNA-seq]

Project description:Single-cell transcriptome profiles of wild-type and IRF8KO microglia [scRNA-seq]

| PRJNA964779 | ENA

Genome-wide methylated CpG status in WT and IRF8KO microglia [WGBS]

Project description:The role of the lineage-determining transcription factor, Interferon regulatory factor (IRF8), in microglia remains elucidated. We report the genome-wide methyl-CpG status in adult wild-type (WT) and IRF8-knockout (IRF8KO) microglia by whole-genome bisulfite-Seq (WGBS). Deep-sequencing and subsequent differential analysis revealed that IRF8KO microglia exhibited a cell-intrinsic methylation profile. Furthermore, the differentially methylated regions showed a significant correlation with IRF8-dependent chromatin accessibility in microglia. This study provides a novel insight into understanding epigenetic regulation in microglia.

2023-06-01 | GSE231404 | GEO

Genome-wide open chromatin status in WT and IRF8KO microglia [ATAC-seq]

Project description:The role of the lineage-determining transcription factor, Interferon regulatory factor (IRF8), in microglia remains unelucidated. We report the genome-wide chromatin status in adult wild-type (WT) and IRF8-knockout (IRF8KO) microglia by ATAC-Seq. Deep-sequencing and subsequent differential analysis revealed that chromatin accessibility in microglia requires IRF8. At the same time, the loss of IRF8 gains aberrant chromatin accessibility that potentially confers mRNA transcription of the genes upregulated in IRF8KO microglia. This study provides a novel insight into understanding epigenetic regulation in microglia.

2023-06-01 | GSE231401 | GEO

Genome-wide open chromatin status in WT and IRF8KO microglia

Project description:The role of a transcription factor, Interferon Regulatory Factor 8 (IRF8), in microglia is yet to be fully understood. We conducted a study to examine the chromatin status of postnatal and adult wild-type (WT) and IRF8-knockout (IRF8KO) microglia through ATAC-Seq. We also added 5xFAD Alzheimer's disease microglia to observe any chromatin events that may be similar in disease-associated microglia. After deep-sequencing and differential analysis, we discovered that chromatin accessibility in microglia is dependent on IRF8. In the absence of IRF8, there was aberrant chromatin accessibility that potentially resulted in mRNA transcription of genes that were upregulated in IRF8KO microglia, which was distinct from 5xFAD microglia. This study contributes to a better understanding of epigenetic regulation in microglia.

2024-07-01 | GSE266421 | GEO

Single-cell transcriptome profiles of wild-type and IRF8KO microglia

Project description:IRF8 is a transcription factor that is crucial in determining the lineage of microglia. We previously showed that IRF8 is robustly bound during the early postnatal period. To better understand IRF8's postnatal functions, we analyzed mice in which IRF8 was removed after P16. By using single-cell nuclei sequencing, we analyzed cells in which IRF8 was definitely knocked out and investigated both the transcriptome and chromatin accessibility that IRF8 regulates. The differential analysis showed the importance of IRF8 in regulating postnatal transcriptional programs and epigenetic landscapes that are related to microglial identity and disease-associated genes. This study provides a new perspective on how IRF8-mediated transcriptional programs affect microglia.

2024-07-01 | GSE266423 | GEO

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