GEO DataSets

(Submitter supplied) Interferon regulatory factor 4 (IRF4) is an IRF family transcription factor with critical roles in lymphoid development and in regulating the immune response. IRF4 binds DNA weakly owing to a carboxy-terminal auto-inhibitory domain, but cooperative binding with factors such as PU.1 or SPIB in B cells increases binding affinity, allowing IRF4 to regulate genes containing ETS–IRF composite elements (EICEs; 5'-GGAAnnGAAA-3'). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL9250 GPL13112 GPL9185

38 Samples

Download data: BED, TXT

(Submitter supplied) Purpose: The purpose of this study is to find the binding partner of IRF4 in the context of Th17- cell differentiation. To this end, we have used ChIPseq analysis followed by de novo motif search around genome-wide binding sites to identify BATF as the binding partner for IRF4 in the context of not only Th17 cells but other immune cell types as well.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11002 GPL13112

9 Samples

Download data: WIG

(Submitter supplied) Transcriptional profiling of T-cells isolated from spleen of IRF4 -/- mice and cultured under Th17 polarizing conditions for 42 hrs compared to cells similarly isolated and cultured from spleen of IRF4 +/- mice. The aim of the study was to identify global misexpression of genes in IRF4 -/- cells and hence identify key pathways regulated by IRF4 during Th17 differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL7202 GPL11002

15 Samples

Download data: TXT, WIG

(Submitter supplied) ChIP-seq data for the transcription factors (TFs) IRF4, PU.1 and SPIB from the cell lines OCI-LY3, OCI-LY10 and H929, and BATF from the cell lines OCI-Ly3 and OCI-Ly10. In addition ChIP-seq for the TFs IRF4, PU.1 and SPIB from the cell line OCI-LY3 following transfections of scramble/SPIB-siRNA.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9115 GPL16791

22 Samples

Download data: BED, BW

(Submitter supplied) Gene expression from OCI-LY3 cells 48hrs after knock down of SPIB.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

4 Samples

Download data: TXT

(Submitter supplied) Gene expression profiling of B-cells from a model differentiation series: from Naïve B-cells, through a proliferative plasmablast stage to long-lived antibody secreting plasma cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

21 Samples

Download data: TXT

(Submitter supplied) Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 172 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform. Classification into GCB, ABC or Type-III subtypes was carried out revealing a significant relationship between subtype and survival.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8432

249 Samples

Download data: TXT

(Submitter supplied) The transcription factor IRF4 regulates immunoglobulin class switch recombination and plasma cell differentiation. Its differing concentrations appear to regulate mutually antagonistic programs of B and plasma cell gene expression. We show IRF4 to be also required for generation of germinal center (GC) B cells. Its transient expression in vivo induced the expression of key GC genes including Bcl6 and Aicda. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL1261

41 Samples

Download data: BED, CEL, FASTA

(Submitter supplied) Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

11 Samples

Download data: BED, FASTA

(Submitter supplied) Temporal analysis of B cell activation in vitro using CD40L and IL-2/4/5 cytokines in wild type Irf4+/+ B cells or in mutant Irf4-/- B cells harboring a tet-inducible allele of Irf4. IRF4 expression was restored, or not, in the Irf4-/- background by culturing in the presence of low or high concentrations of doxycycline. The results provide insight in the role of IRF4 expression levels in coordinating different programs of B cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

30 Samples

Download data: CEL

(Submitter supplied) Batf3 regulates key CD8alpha DC-specific genes.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL17021

109 Samples

Download data

(Submitter supplied) We have examined mechanisms by which Batf acts to initiate gene transcription in developing effector CD4 T cells. We find that in addition to its pioneering function, Batf controls developmentally regulated recruitment of the chromatin architectural factor, Ctcf, to promote chromatin looping that is associated with transcription of lineage-specific genes. The chromatin organizing actions of Batf are largely Ets1-dependent, which appears to be indispensable for the Batf-dependent recruitment of Ctcf. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

10 Samples

Download data: BEDGRAPH

(Submitter supplied) We have examined mechanisms by which Batf acts to initiate gene transcription in developing effector CD4 T cells. We find that in addition to its pioneering function, Batf controls developmentally regulated recruitment of the chromatin architectural factor, Ctcf, to promote chromatin looping that is associated with transcription of lineage-specific genes. The chromatin organizing actions of Batf are largely Ets1-dependent, which appears to be indispensable for the Batf-dependent recruitment of Ctcf. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

30 Samples

Download data: BEDGRAPH

(Submitter supplied) We have examined mechanisms by which Batf acts to initiate gene transcription in developing effector CD4 T cells. We find that in addition to its pioneering function, Batf controls developmentally regulated recruitment of the chromatin architectural factor, Ctcf, to promote chromatin looping that is associated with transcription of lineage-specific genes. The chromatin organizing actions of Batf are largely Ets1-dependent, which appears to be indispensable for the Batf-dependent recruitment of Ctcf. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

69 Samples

Download data: BEDGRAPH

(Submitter supplied) The transcription factor BATF is required for Th17 and TFH differentiation. Here, we show that BATF also has a fundamental role in regulating effector CD8+ T cell differentiation. BATF-deficient CD8+ T cells show profound defects in effector expansion and undergo proliferative and metabolic catastrophe early after antigen encounter. BATF, together with IRF4 and Jun proteins, binds to and promotes early expression of genes encoding lineage-specific transcription-factors (T-bet and Blimp-1) and cytokine receptors, while paradoxically repressing genes encoding effector molecules (IFNg and granzyme B). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

13 Samples

Download data: CEL

(Submitter supplied) The transcription factor BATF is required for Th17 and TFH differentiation. Here, we show that BATF also has a fundamental role in regulating effector CD8+ T cell differentiation. BATF-deficient CD8+ T cells show profound defects in effector expansion and undergo proliferative and metabolic catastrophe early after antigen encounter. BATF, together with IRF4 and Jun proteins, binds to and promotes early expression of genes encoding lineage-specific transcription-factors (T-bet and Blimp-1) and cytokine receptors, while paradoxically repressing genes encoding effector molecules (IFNg and granzyme B). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

23 Samples

Download data: BW

(Submitter supplied) We report the application of ChIP Seq to study the Epstein Barr Virus Nuclear Antigen 3C, an essential transcriptional regulator involved in the transformation of Resting B Lymphocytes to the immortalized Lymphoblast Cell Lines

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL13112

64 Samples

Download data: BIGWIG