GEO DataSets

(Submitter supplied) Inflammatory bowel disease (IBD), characterized by infiltration of polymorphonuclear neutrophils (PMNs), increases the risk of colon cancer. PMN activation corresponds to accumulation of their intracellular Lipid Droplets (LDs). As increased LDs are negatively regulated by transcription factor FOXO3, our aim is to determine the significance of this regulatory network in PMN-mediated IBD and tumorigenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

11 Samples

Download data: XLSX

(Submitter supplied) Obesity, characterized by augmented inflammation and tumorigenesis, is linked to genetic predispositions, such as FOXO3 polymorphisms. As obesity is associated with aberrant macrophages infiltrating different tissue including the colon, we aimed to identify FOXO3-dependent transcriptomic changes in macrophages that drive obesity-mediated colonic inflammation and tumorigenesis. We found that in mouse colons, high-fat-diet-(HFD)-obesity led to diminished FOXO3 levels and increased macrophages. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TSV

(Submitter supplied) Aberrant epithelial differentiation and regeneration contribute to colon pathologies, including inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). Myeloid translocation gene 16 (MTG16, also known as CBFA2T3) is a transcriptional corepressor expressed in the colonic epithelium. MTG16 deficiency in mice exacerbates colitis and increases tumor burden in CAC, though the underlying mechanisms remain unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

42 Samples

Download data: CSV

(Submitter supplied) Background & Aims Activation of the transcription factor nuclear factor-κB (NF-κB) has been associated with the development of inflammatory bowel disease (IBD). Copper metabolism MURR1 domain containing 1 (COMMD1), a regulator of various transport pathways, has been shown to limit NF-κB activation. We investigated the roles of COMMD1 in the pathogenesis of colitis in mice and IBD in human beings.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

12 Samples

Download data: TXT

(Submitter supplied) Forkhead Box O (FOXO) transcription factors are versatile players in diverse cellular processes, affecting tumorigenesis, metabolism, stem cell maintenance and lifespan. To understand the transcriptional output of FOXO3 activation, we investigate features that define the subset of enhancer binding events that actually contribute to gene regulation. We show FOXO3 transcriptional output is determined by the amount of bound FOXO3, which in turn is determined by motif presence, pre-existing enhancer activity and accessibility. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL16288

18 Samples

Download data: BED, RPKM

(Submitter supplied) We combined lineage tracing with single cell RNA sequencing (scRNA-seq) to study the mechanisms underlying the conversion of Paneth cells into bona fide tumor cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: MTX, TSV

(Submitter supplied) To investigate the effect of the cell-of-origin on the transcriptional phenotype of the tumor, we performed bulk RNAseq on macroscopically dissected intestinal tumors from mice carrying lineage-specific Apc/Kras mutations in Paneth or ISC cells. Where indicated, tumorigenisis was triggered in an inflammatory context by administration of Dextran Sodium Sulfate (DSS).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

15 Samples

Download data: TSV

(Submitter supplied) To investigate the effect of wetern-style diet on Paneth cells, we performed bulk RNAseq on sorted Paneth cells from mice fed for 3 months with western-style diet (NWD1) and control diet (AIN76A)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TSV

(Submitter supplied) MicroRNA regulates gene expression. In this experiment, we determined the gene expression changes by the microRNA expression status using Dicer protein nulll. Wildtype, and intermediate expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13915

3 Samples

Download data: TXT

(Submitter supplied) We used microarray to determine the miRNA whose expression was changed at 6 hours after inflammatory cytokines (TNFα, IL1α, IL1β, or IL6) treatment.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL15446

5 Samples

Download data: TXT

(Submitter supplied) FOXO3 is an evolutionally conserved transcription factor that has been linked to longevity. Here we asked whether human stem cells could be functionally enhanced by engineering them to express an activated form of FOXO3. This was accomplished via HDAdV-mediated gene editing of human embryonic stem cells. These cells were then differentiated into a range of vascular cell types, as FOXO3 has been shown to play a protective role in the cardiovascular system. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

81 Samples

Download data: TXT, WIG

(Submitter supplied) Inflammation is a significant risk factor for colon cancer. Recent work has demonstrated essential roles for several infiltrating immune populations in the metaplastic progression following inflammation. Hypoxia and stabilization of hypoxia-inducible factors (HIFs) are hallmark features of inflammation and solid tumors. Previously, we demonstrated an important role for tumor epithelial HIF-2α in colon tumors; however, the function of epithelial HIF-2α as a critical link in the progression of inflammation to cancer has not been elucidated. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT

(Submitter supplied) To investigate the detailed molecular mechanisms for the regulatory role of HIF-1α in colon, microarray gene expression analysis was performed on colon RNA isolated from 6- to 8-week-old Hif-1α+/+, Hif-1αLSL/LSL mice. Background & Aims: The progression and growth of solid tumors leads to a state where tumors outgrow their capacity for efficient oxygenation and nutrient uptake and an increase in tumor hypoxia. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

2 Samples

Download data: CEL

(Submitter supplied) In this study, using single cell RNAseq, cell mass-spectrometry, flow cytometry, and functional analysis, we characterized the heterogeneity of polymorphonuclear neutrophils (PMN) in cancer. We described three populations of PMN in tumor-bearing mice: classical PMN, polymorphonuclear myeloid derived suppressor cells (PMN-MDSC), and activated PMN-MDSC with potent immune suppressive activity. In spleens of mice, PMN-MDSC gradually replaced PMN during tumor progression. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL19057

13 Samples

Download data: MTX, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL81 GPL1261

81 Samples

Download data: CEL

(Submitter supplied) The process of liver regeneration can be divided into a series of stages that include initial inductive or priming events through cellular mitosis. Following two-thirds liver resection, the liver undergoes the “priming” phase, in which cytokines TNF-a and IL-6 activate their respective receptors in hepatocytes. This leads to the activation of several key transcription factors: NF-kB, AP-1, Stat 3, Stat 1, and C/EBP-b and -d . more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

35 Samples

Download data: CEL

(Submitter supplied) The process of liver regeneration can be divided into a series of stages that include initial inductive or priming events through cellular mitosis. Following two-thirds liver resection, the liver undergoes the “priming” phase, in which cytokines TNF-a and IL-6 activate their respective receptors in hepatocytes. This leads to the activation of several key transcription factors: NF-kB, AP-1, Stat 3, Stat 1, and C/EBP-b and -d . more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL81

46 Samples

Download data: CEL

(Submitter supplied) Forkhead box class O (FoxO) transcription factors regulate whole body energy metabolism, skeletal muscle mass and substrate switching. To elucidate the role of FOXO in skeletal muscle, dominant negative (dn) constructs for FOXO1 (FOXO1dn) or FOXO3 (FOXO3dn) were transfected by electroporation into mouse tibialis anterior muscle and glucose uptake, signal transduction, and glucose stimulated gene expression profiles were assessed. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17400

24 Samples

Download data: CEL

(Submitter supplied) The DNA binding factor Tcf-1 is one of the most prominently expressed genes in thymocytes yet its global DNA binding pattern remained unknown. Here we have assessed by ChIP-seq the Tcf-1 binding pattern in murine thymocytes in WT B6 mice and in mice expressing a stabilized form of the Tcf-1 binding partner beta-Catenin (CAT mice).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: WIG

(Submitter supplied) There is much controversy about the role of T-regulatory cells (Treg) in human colon cancer. High densities of tumor-infiltrating Treg can correlate with better or worse clinical outcomes depending on the sutdy. Treg have potent anti-inflammatory functions that have been shown to control cancer progression. However, Treg isolated from patient with colon cancer or in mouse models of polyposis do not have the ability to suppress inflammation and instead promote cancer. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4588

Platform:

GPL6246

44 Samples

Download data: CEL