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IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs

ABSTRACT: IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs

PROVIDER: PRJNA964768 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24389800_1.fastq.gz	Fastqsanger.gz
	SRR24389800_2.fastq.gz	Fastqsanger.gz
	SRR24389838_1.fastq.gz	Fastqsanger.gz
	SRR24389838_2.fastq.gz	Fastqsanger.gz
	SRR24389839_1.fastq.gz	Fastqsanger.gz

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IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs - additional datasets

Project description:IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs - additional datasets

| PRJNA1107149 | ENA

IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs

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

2023-06-01 | GSE231406 | GEO

IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs - additional datasets

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

2024-07-01 | GSE266424 | GEO

Genome-wide profiles of IRF8 and PU.1 bindings, and H3K4me1 and H3K27ac histone marks in wild-type and IRF8-knockout microglia [CHIP-seq]

Project description:The role of the lineage-determining transcription factor Interferon regulatory factor 8 (IRF8) in microglia remains elucidated. Here we report the genome-wide IRF8 binding profiles in microglia at various ages. CUT&RUN methodology revealed that IRF8 starts to bind to the genome around postnatal day 9 (P9), and its number increases with age. In comparison to peritoneal macrophages, microglia IRF8 showed a cell-intrinsic binding pattern. By co-occurrence analysis, most IRF8 was H3K4me1/H3K27ac-marked enhancers, and many of them bind to the H3K27ac(high) super-enhancer regions. In IRF8KO microglia, H3K4me1 and H3K27ac profiles were altered and deposited aberrantly on the genome. This study provides a novel insight into understanding epigenetic regulation in microglia.

2023-06-01 | GSE231402 | GEO

Gene expression analyses in IRF8-induced monocyte differentiation

Project description:To understand the differentiation program in monocyte/macrophage differentiation, we performed ChIP-seq for IRF8 and H3K4me1 together with gene expression profiling during IRF8-induced monocyte differentiation. Both promoter-proximal and -distal binding of IRF8 associated with induction of the genes especially those related to monocytes/macrophages and immunity. DNA motif analysis for cis-regulatory elements of indirect IRF8 target genes predicted KLF4, essential for Ly6C+ monocyte development, to be a downstream transcription factor regulating the indirect target gene expression. Introduction of KLF4 into an Irf8-/- myeloid progenitor cell line induced a subset of IRF8 target genes and partially induced monocyte/macrophage differentiation. Together, this study revealed the genome-wide behavior of IRF8 and the IRF8-KLF4 axis during monocyte differentiation. Gene expressions in monocyte-like cells differentiated by IRF8 or KLF4 were measured at day 4 after retroviral transductions to myeloid progenitor cell line, Tot2. Two independent experiments were performed.

2013-01-24 | E-GEOD-38810 | biostudies-arrayexpress

IRF8-regulated genes in primary CD11 b cells

Project description:Transcriptional profiling of IRF8-regulated genes in mouse CD11b-positive primary cells. CD11b-positive cells were isolated from spleens of age-matched wt and IRF8 KO mice, the compared for their gene expression profiles. The objective is to identify genes that are regulated by IRF8 in CD11b-positive primary cells. Two-condition experiments. Wt vs IRF8 KO cells. Biological replicates: 2 replicates for the comparison.

2011-10-19 | E-GEOD-31464 | biostudies-arrayexpress

Gene expression analyses in IRF8-induced monocyte differentiation

2013-01-24 | GSE38810 | GEO

Chip-chip from human diffuse large B cell lymphoma cell lines with IRF8

Project description:IRF8, a transcriptional factor, has the heightened expression in germinal center(GC) B cell and GC-origin B cell lymphoma. To identify IRF8 direct targets in GC B cells, ChIP-chip ananlysis was done in three different GC-origin diffuse large B cell lymphoma cell lines. IRF8-negative cell lines, MMS1, was also used as a negatvie control. IRF8 ChIP in three different cell lines (ODH1, VAL and LY1:high level of IRF8) and in one negative control cell lines (MMS1:negatvie for IRF8). Total four different samples. One sample per a set of two arrays (promoter1 and promoter2).

2011-10-14 | E-GEOD-30357 | biostudies-arrayexpress

Chip-chip from mouse diffuse large B cell lymphoma cell lines with IRF8

Project description:IRF8, a transcriptional factor, has the heightened expression in germinal center(GC) B cell and GC-origin B cell lymphoma. To identify IRF8 direct targets in GC B cells, ChIP-chip ananlysis was done in three different GC-origin diffuse large B cell lymphoma cell lines. IRF8-negative cell lines, MPC11, was also used as a negatvie control. IRF8 ChIP in three different cell lines (NFS201, NFS202 and NFS205:high level of IRF8) and in one negative control cell lines(MPC11:negatvie for IRF8). Total four different samples. One sample per a set of two arrays (promoter1 and promoter2).

2011-10-14 | E-GEOD-30519 | biostudies-arrayexpress

IRF8 REGULATES EXPRESSION OF ANTIGEN PROCESSING AND PRESENTATION PATHWAYS IN MYELOID CELLS

Project description:In this study, we have used transcript profiling with microarrays in bone marrow-derived macrophages (BMDMs) to systematically identify genes transcriptionally regulated by IRF8 during ontogeny and maturation of macrophages, and in response of these cells to combined exposure to IFNgamma and Tlr9 ligand (CpG). For this, we used an experimental strategy based on the co-segregation of IRF8-dependent differential gene expression in macrophages from [BALB/c X BXH2] F2 animals selected for homozygosity for either wild type (wt; IRF8R294) or mutant (IRF8C294) IRF8 alleles. The study of IRF8-associated gene expression differences in individual animals of mixed genetic background, allows one to distinguish true IRF8-dependent effects on gene expression from unrelated differences in gene expression associated with intrinsic differences in genetic background but unrelated to IRF8.

2011-04-27 | E-MEXP-2962 | biostudies-arrayexpress

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