GEO DataSets

(Submitter supplied) We found that Ikaros is critical to limit the expression of pro-inflammatory cytokines in TCR/CD28-activated CD4+ T cells. To understand if Ikaros could modify the chromatin accessibility in regions controling the expression of these pro-inflammatory genes, we examined the chromatin state in naive CD4+ T cells and CD4+ T cells activated with anti-CD3+anti-CD28 antibodies for 1 and 2 days, from WT (Ikaros f/f CD4-Cre-) and Ikaros TKO mice (Ikaros f/f CD4-Cre+), using the ATAC-seq approach.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: BIGWIG

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

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

40 Samples

Download data: BIGWIG, BW

(Submitter supplied) The aim of the project is to determine the binding sites of Ikaros in CD4+ T cells. To perform this, CD4 naive T cells (CD4 TN; d0) either rested or activated with anti-CD3+anti-CD28 Abs for 1 day (Th0 d1) were subjected to a ChIP using anti-Ikaros Ab followed by high throughput sequencing.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: BW

(Submitter supplied) We found by microarray analysis that Ikaros is critical to limit the expression of several pro-inflammatory genes during Th17 cell polarization. To unravel the role of Ikaros in the expression of pro-inflammatory genes without Th17 polarizing cytokines, we performed an RNA-seq analysis in naive CD4+ T cells and CD4+ T cells activated with anti-CD3+anti-CD28 antibodies (Th0 condition), from WT (Ikaros f/f CD4-Cre-) and Ikaros TKO mice (Ikaros f/f CD4-Cre+).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: TSV

(Submitter supplied) We found that CD4+ T cells require Ikaros to promote IL-17 production when cultured in Th17 conditions. To understand why Ikaros null T cells do not produce IL-17, we analyzed the transcriptome of WT vs. Ikaros null naive CD4+ T cells both resting (day 0) or activated with anti-CD3 plus anti-CD28 antibodies, IL-6, TGFb1 and neutralizing anti-IFNg and anti-IL-4 antibodies (Th17 condition) for 1 or 2 days. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

18 Samples

Download data: CEL

(Submitter supplied) GM-CSF positve CD4 cells are found at sites of inflammation. The purpose of this study was to understand their transcriptional profile relative to known Th1 and Th17 subsets.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: TXT

(Submitter supplied) To investigate the effects of a late deletion of Gata3 on CD4 T cell gene expression profiles in experimental autoimmune encephalomyelitis, we performed a RNA-Seq analysis of Gata3-sufficient (i.e., Cd45.1/Cd45.2 or vehicle treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 fl/fl) and Gata3-deficient (i.e., tamoxifen-treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl) CNS-infiltrating CD4+ effector T cells from mixed congenic co-transfer recipient mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

8 Samples

Download data: TXT

(Submitter supplied) We showed that the transcription factor Foxo3 played a specific role in the polarization of CD4+ T cells towards pathogenic Th1 cells producing both interferon-γ (IFN-γ) and granulocyte monocyte colony stimulating factor (GM-CSF). To understand the molecular mechanisms whereby Foxo3 controls CD4+ T cell differentiation, unbiased analysis of genes differentially expressed in Foxo3-deficient vs. Foxo3-sufficient CD4+ T cells was achieved using both resting and activated CD4+ T cells obtained following 12 or 24 hours of stimulation with anti-CD3 mAbs.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

22 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL9250

46 Samples

Download data: BIGWIG, BW

(Submitter supplied) Ikaros encodes a transcription factor that functions as a tumor suppressor in T-ALL. The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells results in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic global epigenomic and gene expression analyses to determine the role of Ikaros in tumor suppression during this process. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL9250

38 Samples

Download data: BW

(Submitter supplied) Ikaros encodes a transcription factor that functions as a tumor suppressor in T-ALL. The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells results in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic global epigenomic and gene expression analyses to determine the role of Ikaros in tumor suppression during this process. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: BIGWIG

(Submitter supplied) Ikaros was found to antagonize the transcriptional program of IL-7 activated pathways during pre-B cell differentiation. We analyzed the genomic distribution of Ikaros and STAT5 (downstream effector of IL-7; in the presence or absence of Ikaros) in pre-B cells by ChIP-Seq.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: WIG

(Submitter supplied) The aim of the experiment was to compare to single and combined effect of Ikaros activation and IL-7 withdrawal in the Ikaros-null pre-B cell line BH1

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

14 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

43 Samples

Download data: BEDGRAPH, CSV, FPKM_TRACKING

(Submitter supplied) Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor families. Here we describe an unexpected role for the lymphoid lineage-determining factor Ikaros in the macrophage LPS response using comprehensive genomic analysis of Ikaros-dependent transcription, DNA binding, and chromatin accessibility. Ikaros exhibited dual repressor and activator roles in LPS-induced gene expression. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor families. Here we describe an unexpected role for the lymphoid lineage-determining factor Ikaros in the macrophage LPS response using comprehensive genomic analysis of Ikaros-dependent transcription, DNA binding, and chromatin accessibility. Ikaros exhibited dual repressor and activator roles in LPS-induced gene expression. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor families. Here we describe an unexpected role for the lymphoid lineage-determining factor Ikaros in the macrophage LPS response using comprehensive genomic analysis of Ikaros-dependent transcription, DNA binding, and chromatin accessibility. Ikaros exhibited dual repressor and activator roles in LPS-induced gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

16 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Interleukin-21 (IL-21) has broad actions on T- and B-cells, but its actions in innate immunity are poorly understood. Here we show that IL-21 induced apoptosis of conventional dendritic cells (cDCs) via STAT3 and Bim, and this was inhibited by granulocyte-macrophage colony-stimulating factor (GM-CSF). ChIP-Seq analysis revealed genome-wide binding competition between GM-CSF-induced STAT5 and IL-21-induced STAT3. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

6 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

112 Samples

Download data

(Submitter supplied) Above primary T cell subsets were isolated by magnetic isolation (including GM-CSF capture and secretion assay) from peripheral blood of 5 to 6 human healthy donors. Total RNA (and genomic DNA for an accompanying dataset) was extracted for transcriptome analysis. By integration of RNA-seq data with corresponding ATAC-seq data we generated a novel gene regulatory network of human GM-CSF producing and memory T helper cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

29 Samples

Download data: TXT