GEO DataSets

(Submitter supplied) Goal: Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the longitudinal axis, contributes to a differential response to chemoprotective agents. Method: We assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. more...

Organism:

Rattus norvegicus

Type:

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

Platform:

GPL14844

7 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) In an effort to gain insight into the extensive dimension of post-translational modifications in histones (including H3K4me3 and H3K9ac) and elucidate the chemoprotective impact of dietary bioactive compounds on transcriptional control in a colon cancer preclinical model, we generated high-resolution genome-wide RNA (RNA-Seq) and “chromatin-state” (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed bioactive (i) fish oil (ii) butyrate (in the form of a fermentable fiber a rich source of SCFA), (iii) a combination of fish oil plus butyrate or (iv) control diets. more...

Organism:

Rattus norvegicus

Type:

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

Platform:

GPL18694

107 Samples

Download data: XLS

(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 high throughput sequencing

Platform:

GPL10999

24 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Dramatic changes of gene expressions are known to occur in human endometrial stromal cells (ESC) during decidualization. The changes in gene expression are associated with changes of chromatin structure, which are regulated by epigenetic mechanisms such as histone modifications. Here, we investigated genome-wide changes in histone modifications and mRNA expressions associated with decidualization in human ESC using chromatin immunoprecipitation (ChIP) combined with next-generation sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: TXT

(Submitter supplied) Dramatic changes of gene expressions are known to occur in human endometrial stromal cells (ESC) during decidualization. The changes in gene expression are associated with changes of chromatin structure, which are regulated by epigenetic mechanisms such as histone modifications. Here, we investigated genome-wide changes in histone modifications and mRNA expressions associated with decidualization in human ESC using chromatin immunoprecipitation (ChIP) combined with next-generation sequencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

20 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) A genome-wide integrated methylome and transcriptome analysis of the early stage of hepatocellular carcinoma development that induced by HBx. The HBV x (HBx) protein, which plays a critical role in the development of HCC, was shown to interact with several epigenetic factors, such as DNMT3A and HDAC1. Most HBx transgenic (TG) mice spontaneously develop HCC at about 1 year of age, providing genetic validation of the oncogenic potential of HBx even in the absence of viral integration and chronic inflammation. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: RPKM

(Submitter supplied) Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) was then performed to establish the H3K4me3 landscape in neonatal and adult CD14+ monocytes. As development progressed from neonate to adult, monocytes gained the activating mark H3K4me3. The decreased H3K4me3 abundance at immunologically important neonatal monocyte gene promoters correlated with reduced gene expression, providing evidence that neonatal immune cells exist in an epigenetic state that is distinctly different from adults, and that this state contributes to neonatal specific immune responses.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

24 Samples

Download data: BED

(Submitter supplied) Epigenetic profiling of DNA methylation, histone H3 lysine 4 trimethylation and histone H3 lysine 9 trimethylation at imprinted gene clusters in the mouse.

Organism:

Mus musculus

Type:

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

Platform:

GPL8714

18 Samples

Download data: TXT

(Submitter supplied) We previously reported that lifetime consumption of soy proteins or whey proteins reduced the incidence of azoxymethane (AOM)-induced colon tumors in rats. To obtain insights into these effects, global gene expression profiles of colons from rats with lifetime ingestion of casein (CAS, control diet), soy protein isolate (SPI), and whey protein hydrolysate (WPH) diets were determined. We identified 31 induced and 49 repressed genes in the proximal colons of the SPI-fed group and 44 induced and 119 repressed genes in the proximal colons of the WPH-fed group, relative to CAS. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS2468

Platform:

GPL85

9 Samples

Download data: CEL, EXP

Analysis of colons of soy or whey protein fed Sprague Dawley males 40 weeks after azoxymethane (AOM) injection to induce tumor formation. Lifetime consumption of soy or whey proteins reduces the incidence of AOM-induced colon tumors in rats.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL85

Series:

GSE6102

9 Samples

Download data: CEL, EXP

(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

12 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes up-regulated in abdominal preadipocytes and 90 genes up-regulated in GF cells. Assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200kb of the transcription start site (TSS). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes up-regulated in abdominal preadipocytes and 90 genes up-regulated in GF cells. Assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200kb of the transcription start site (TSS). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: XLSX

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL198 GPL9062

12 Samples

Download data: CEL, TAR, XLS

(Submitter supplied) These ChIP-seq data files are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Keywords: stress response, histone modification

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: TAR, XLS

(Submitter supplied) These microarrays are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels (via ChIP-seq) in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Water deficit stress causes a large number of genes to change their transcript levels, which provided a large set of genes to examine for corresponding chromatine changes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) loss of Men1 in mouse pancreatic islet cells alters the epigenetic landscape of a subset of target genes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: BED

(Submitter supplied) We report a computational approach for investigation of chromatin state plasticity. We applied this approach to investigate an ENCODE ChIP-seq dataset profiling the genome-wide distribution of H3K27me3 in 19 human cell lines. We found that high plasticity regions (HPRs) can be divided into two functionally and mechanistically distinct groups, consisting of CpG island proximal and distal regions. We identified cell-type specific regulators correlating with H3K27me3 patterns at distal HPRs in ENCODE cell lines. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL14761

6 Samples

Download data: BED, WIG

(Submitter supplied) Within the cell nucleus, histone H1 is the most mobile histone. Yet, it is regarded as key to the establishment and stability of chromatin higher-order structure. The implication is that chromatin higher-order structure is dynamic, in part due to the mobility of H1. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq) is traditionally the method for mapping histones onto DNA elements. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: BED, BW, TDF