GEO DataSets

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived interferon-stimulated MEF cells transcriptome profiling (RNA-seq).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL6246 GPL13112

60 Samples

Download data: CEL, CHP, WIG

(Submitter supplied) We have analyzed epigenetic state of interferon stimulated cells and found that histone H3.3 and H3K36me3 chromatin marks were increased to regulate transcriptional memory.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

34 Samples

Download data: WIG

(Submitter supplied) We used global microarray analysis to identify genes which are regulated by Interferon-gamma stimulation in Bone-marrow derived macrophages.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

16 Samples

Download data: CEL, CHP

(Submitter supplied) The antiviral response induced by type I interferon (IFN) via the JAK-STAT signaling cascade results in the activation of a set of IFN-stimulated genes (ISGs). This response varies between different cell types of the organism. However, the linkage between the underlying epigenetic features and innate immune response is not well understood. We mapped ISGs and STAT1 and STAT2 binding sites in mouse embryonic stem cells and differentiated cells before and after treatment with IFNβ together with histone acetylation (ac) and mono- and tri-methylation (me1, me3) marks at histone H3 lysine residues for H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K9me3 and H3K27me3. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL13112 GPL21103

221 Samples

Download data: BED, MTX, TAR, TSV, 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 genome tiling array

9 related Platforms

37 Samples

Download data: CEL

(Submitter supplied) Immunological memory is generally thought to be mediated exclusively by lymphocytes such as memory T and B cells. However, enhanced innate immune responses caused by a previous infection increase protection against reinfection suggesting the presence of innate immunological memory. Here, we describe 3,811 ATF7 binding sites in mouse peritoneal macrophages, and 95% of the ATF7 signals in wild-type macrophages are lost in ATF7 knockout macrophages. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

8 related Platforms

9 Samples

Download data: BED, CEL

(Submitter supplied) Immunological memory is generally thought to be mediated exclusively by lymphocytes such as memory T and B cells. However, enhanced innate immune responses caused by a previous infection increase protection against reinfection suggesting the presence of innate immunological memory. Here, we describe expression profile of peritoneal macrophages from wild-type mice pre-administrated with TLR ligands or from ATF7 knockout mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

28 Samples

Download data: CEL

(Submitter supplied) mRNA from wild-type (Cre-) and MLL1-deficient (Cre+) BMDMs were analyzed via gene chip (Mouse Gene ST 2.1, Affymetrix) for relative expression changes. Isolated mRNA from Cre- and Cre+ BMDMs stimulated with classical activation signals (IFNg, LPS or IFNg+LPS) was analyzed using a gene chip panel of >40,000 RefSeq transcripts, and resulting fold expression was determined by analyzing quality-controlled expression values for validated probesets.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17400

24 Samples

Download data: CEL

(Submitter supplied) Identification of RNAs differentially expressed upon ZFR knockdown in THP1 and HEK-293TO cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21290 GPL11154

18 Samples

Download data: DAT, TXT

(Submitter supplied) Interpretation of genome-wide investigations of host-pathogen interactions are often obscured by analyses of mixed populations of infected and uninfected cells. Thus, we developed a system whereby we simultaneously characterize and compare genome-wide transcriptional and epigenetic changes in pure populations of virally-infected and neighboring uninfected cells to identify viral-regulated host-responses. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL18573

60 Samples

Download data: BED, TXT

(Submitter supplied) This in-vitro study suggests the inflammatory environment of naive epithelial cells can induce epigenetic modulation of innate immune responses at the level of histone methylation and potentially lead to long-term impacts on anti-viral immunity.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 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; Expression profiling by high throughput sequencing

Platform:

GPL13112

35 Samples

Download data: BW

(Submitter supplied) To indentify genes displaying long-term transcriptionnal memory (LTTM) we used a trans-differentiation system where Bcell are reprogramed into macrophages upon induction of the transcription factor Cebpa. We performed RNAseq in untreated Bcells, after 12h of Cebpa induction and after 6days of “wash” of Cebpa, to see if any genes respond more/faster in a second stimulation than in the first.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: BW

(Submitter supplied) To investigate the epigenetic control of long-term transcriptionnal memory (LTTM) we used a trans-differentiation system where Bcell are reprogramed into macrophages upon induction of the transcription factor Cebpa. We performed ChIPseq in untreated Bcells, after 12h of Cebpa induction and after 6days of “wash” of Cebpa, to see if any proteins/histone marks are retained.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

17 Samples

Download data: BW

(Submitter supplied) The goal of this study was to investigate whether histone modifcations and gene expression changes in mouse macrophages induced by beta glucan could persist over the course of many cell divisions following stimulus removal

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL23969

376 Samples

Download data: CSV

(Submitter supplied) Microglia are the tissue-resident macrophages of the CNS. They originate in the yolk sac, colonize the CNS during embryonic development and form a self-sustaining population with limited turnover. A consequence of their relative slow turnover is that microglia can serve as a long-term memory for inflammatory or neurodegenerative events. We characterized the epigenomes and transcriptomes of microglia exposed to different stimuli; an endotoxin challenge (LPS) and genotoxic stress (DNA repair deficiency-induced accelerated aging). more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL17021

54 Samples

Download data: NARROWPEAK, TSV, TXT

(Submitter supplied) Known for nearly a century, but through mechanisms that remain elusive, cells retain a memory of inflammation that equips them to react quickly and broadly to diverse secondary stimuli. Using mouse epidermal stem cells as a model, we elucidate how cells establish, maintain and recall inflammatory memory. Specifically, we landscape and functionally interrogate temporal, dynamic changes to chromatin accessibility, histone modifications and transcription factor binding that occur during inflammation, post-resolution and in memory recall following injury. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL19057 GPL17021

146 Samples

Download data: BED, TXT