GEO DataSets

(Submitter supplied) Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS). To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches - gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

18 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL9052 GPL5175

26 Samples

Download data: BED, CEL

(Submitter supplied) Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS). To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches - gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

8 Samples

Download data: CEL

(Submitter supplied) Innate immune response to pathogens is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of the response to LPS have been identified, the temporal complexity of gene expression changes strongly suggest that additional layers of regulation remain to be uncovered. This study was done to examine response of mouse bone marrow-derived macrophages to stimulation with LPS over time. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23585

12 Samples

Download data: CEL

(Submitter supplied) Hyperglycemia is an essential factor leading to micro- and macrovascular diabetic complications. Macrophages are key innate immune regulators of inflammation that undergo 2 major directions of functional polarization: classically (M1) and alternatively (M2) activated macrophages. The aim of the study was to examine the effect of hyperglycemia on transcriptional activation of M0, M1 and M2 human macrophages.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20171

24 Samples

Download data: CEL

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

Organism:

Rattus norvegicus

Type:

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

Platforms:

GPL10669 GPL4135

18 Samples

Download data: BED, TXT, WIG

(Submitter supplied) PAX8 transcriptional profiling of rat PCCL3 cells comparing wild type cells with PAX8 silenced cells and scramble treated with PAX8 silenced cells

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL4135

16 Samples

Download data: TXT

(Submitter supplied) Analysis of PAX8 binding sites by chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq) in PCCL3 rat cells. Results provide insight into the contribution of this regulatory factor to transcription genome-wide.

Organism:

Rattus norvegicus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10669

2 Samples

Download data: BED, WIG

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

Organism:

Gallus gallus

Type:

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

Platform:

GPL21224

4 Samples

Download data: BIGWIG

(Submitter supplied) Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that immune genes were associated with H3K4me3 and H3K27ac. In conjunction with next-generation DNA, RNA sequencing, chromatin immunoprecipitation-DNA sequencing and FAIRE sequencing, we identified the active chromosomal compartments and determined their structural signatures in relation to expression levels.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21224

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that immune genes were associated with H3K4me3 and H3K27ac.Our data provide a genome-wide profile of chromatin signatures for immune genes in chicken polychromatic erythrocytes.

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21224

2 Samples

Download data: BIGWIG

(Submitter supplied) Paeony root has long been used for its anti-inflammatory effects. In this study, the effects of albiflorin, paeoniflorin, and paeonol, compounds from paeony root, on gene expression profiles were examined in macrophages. The RAW264.7 macrophages were treated with LPS in the presence or absence of albiflorin, paeoniflorin, or paeonol. Global mRNA expression levels were detected by using an oligonucleotide microarray platform covering the mouse whole genome. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2995

33 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; Expression profiling by high throughput sequencing

4 related Platforms

55 Samples

Download data: BED, FA, TXT

(Submitter supplied) Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Using a combination of genome-wide and gene-specific approaches, we provide evidence that rather than representing off/on transitions, Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early (I/E) and late response genes results from a sequential process in which signal-independent factors, exemplified by Gabpa, initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6100

8 Samples

Download data: TXT

(Submitter supplied) Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Using a combination of genome-wide and gene-specific approaches, we provide evidence that rather than representing off/on transitions, Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early (I/E) and late response genes results from a sequential process in which signal-independent factors, exemplified by Gabpa, initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

24 Samples

Download data: TXT

(Submitter supplied) Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Using a combination of genome-wide and gene-specific approaches, we provide evidence that rather than representing off/on transitions, Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early (I/E) and late response genes results from a sequential process in which signal-independent factors, exemplified by Gabpa, initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL9250 GPL9185

23 Samples

Download data: BED, FA, 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:

GPL10787 GPL11002

12 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Chromatins were prepared from myeloid progenitor cell line Tot2 cells transduced with retrovirus for control MSCV or MSCV-IRF8. Chromatin immunoprecipitation (ChIP) was carried out by using anti-IRF8 antibody, anti-PU.1 antibody or anti-histone H3K4me1 antibody. ChIP-Seq peaks were identified using the FindPeaks tool in the HOMER package or SICER with input DNA tags as background distribution. Potential IRF8-direct target genes were identified based on ChIP-Seq and the alteration of expression by IRF8-induction.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BEDGRAPH

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

6 Samples

Download data: TXT

(Submitter supplied) Chromatin accessibility is a key determinant of cell-type-specific gene expression. Here, we have investigated the chromatin architecture of different acute myeloid leukemia (AML) cells and the changes in accessibility when NB4 (APL) cells undergo the process of differentiation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

25 Samples

Download data: BED, WIG