GEO DataSets

(Submitter supplied) Unraveling the complexity of transcriptional programs coded by different cell types has been one of the central goals of cell biology. Using genome-wide location analysis, we examined how two different cell types generate different responses to the NF-kappaB signaling pathway. We showed that, after tumor necrosis factor-alpha (TNF-alpha) treatment, NF-kappaB p65 subunit binds to distinct genome locations and subsequently induces different subsets of genes in human monocytic THP-1 cells versus HeLa cells . more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

4 related Platforms

72 Samples

Download data: PAIR

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

5 related Platforms

82 Samples

Download data: CEL, PAIR

(Submitter supplied) Unraveling the complexity of transcriptional programs coded by different cell types has been one of the central goals of cell biology. Using genome-wide location analysis, we examined how two different cell types generate different responses to the NF-kappaB signaling pathway. We showed that, after tumor necrosis factor-alpha (TNF-alpha) treatment, NF-kappaB p65 subunit binds to distinct genome locations and subsequently induces different subsets of genes in human monocytic THP-1 cells versus HeLa cells . more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

10 Samples

Download data: CEL

(Submitter supplied) Recent studies suggest a hierarchical model in which lineage-determining factors act in a collaborative manner to select and prime cell-specific enhancers, thereby enabling signal-dependent transcription factors to bind and function in a cell type-specific manner. Consistent with this model, TLR4 signaling primarily regulates macrophage gene expression through a pre-existing enhancer landscape. However, TLR4 signaling also induces priming of ~3000 enhancer-like regions de novo, enabling visualization of intermediates in enhancer selection and activation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL9250 GPL13112

139 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Cellular differentiation is orchestrated by lineage-specific transcription factors and associates with cell type-specific epigenetic signatures. Here, we utilized stage-specific, epigenetic "fingerprints" to deduce key transcriptional regulators of a cellular differentiation process. In the model of human macrophage differentiation, we globally mapped the distribution of epigenetic enhancer marks (histone H3 lysine 4 monomethylation, histone H3 lysine 27 acetylation, and the histone variant H2AZ) and show that cell type-specific epigenetic "fingerprints" correlate with specific, de novo derived motif signatures at all differentiation stages studied (hematopoietic progenitor cell, monocyte, macrophage). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

13 Samples

Download data: BED, TXT

(Submitter supplied) Conversion of cytokine-driven changes in chromatin topology into gene regulatory circuits during inflammation still remains unclear. Here, we analyzed the expression profiles of HeLa cells carrying microdeletions of p65-binding sites in two enhancers regulating the IL-1α-inducible IL8 and CXCL1-3 genes within the extended chemokine locus on human chromosome 4.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

20 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL13497

32 Samples

Download data: BIGWIG, BW, TXT

(Submitter supplied) The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of CTCF by ChIP-seq experiments.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: BW

(Submitter supplied) The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the chromatin accessibilty at the genome-wide level by ATAC-seq experiments.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BIGWIG

(Submitter supplied) Myeloid cells of the granulocytic-monocytic (GM) lineage develop in a process orchestrated mainly by the transcription factors PU.1 and CEBPA, but how these factors collaborate on a global scale during GM-lineage differentiation remains uncharacterized. To address this question we have combined epigenetic profiling, transcription factor binding and gene expression analyses of successive stages of murine GM-lineage differentiation and show that PU.1 and CEBPA binds to GM enhancers with distinct kinetics. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

77 Samples

Download data: BEDGRAPH, BW, TXT