GEO DataSets

(Submitter supplied) On going efforts are directed at understanding the mutualism between the gut microbiota and the host in breast-fed versus formula-fed infants. Due to the lack of tissue biopsies, no investigators have performed a global transcriptional (gene expression) analysis of the developing human intestine in healthy infants. As a result, the crosstalk between the microbiome and the host transcriptome in the developing mucosal-commensal environment has not been determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2895

12 Samples

Download data: TXT

(Submitter supplied) We developed a non-invasive ex vivo HT29 cell-based minimal model to fingerprint the mucosa-associated microbiota fraction in humans. HT29 cell-associated fractions were characterized by the universal phylogenetic array platform HTF-Microbi.Array, both in presence or in absence of a TNF-α-mediated pro-inflammatory stimulus.

Organism:

synthetic construct; human gut metagenome

Type:

Other

Platform:

GPL17770

90 Samples

Download data: CSV

(Submitter supplied) Conventionally raised and germ-free newly weaned male Sprague-Dawley rats were fed a basal diet or a diet supplemented with digestion resistant carbohydrates in the form of inulin, resistant starch or konjac flour. Gene expression in colon tissue was measured to characterise interaction between food, microbes and host.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL4135

41 Samples

Download data: TXT

(Submitter supplied) Molecular adaptation of the intestinal mucosa occurs during microbial conventionalization to maintain a balanced immune response. However, the genetic regulation of such adaptation is obscure. Here, combined analysis of germ free and conventionalized mice revealed that the major molecular adaptations were initiated at day 4 of conventionalization with a strong induction of innate immune functions followed by stimulation of adaptive immune functions. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4319

Platform:

GPL11533

144 Samples

Download data: CEL

Temporal analysis of colon, ileum, and jejunum from conventionalized males (i.e., germfree mice colonized with total fecal microbiota of their conventionally born and raised siblings). Results provide insight into molecular basis of innate and adaptive immune responses during conventionalization.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 protocol, 7 time, 3 tissue sets

Platform:

GPL11533

Series:

GSE32513

144 Samples

Download data: CEL

(Submitter supplied) Increase of fecal hazardous compounds and decrease of butyrate-producing bacteria has been implicated to be detrimental to colonic health during weight loss by high-protein diet in human. The question remains that whether the change of luminal microenvironment were paralleled with the alteration of colonic function in vivo.To reveal the change of gene expression involved in metabolic or immmunological process, we have employed the whole genome microarray profiling to identify differentially expressed genes in rat dietary normal protein (20% protein) or high protein (45% protein) diet. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL14746

12 Samples

Download data: TXT

(Submitter supplied) The lean and fat broilers were derived from the 21st generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). In brief, broilers in the two lines (lean line and fat line) of the NEAUHLF have the same Arbor Acres ancestry, but were divergently selected by the concentration of very low-density lipoprotein and abdominal fat percentage (AFP) at 7 weeks old. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

80 Samples

Download data: TXT

(Submitter supplied) Impact of antibiotics (T2) or antibiotics in combination with stress (T3) in early life on intestinal functioning in pigs on 8, 55, 176 days in jejunum and ileum (blood only day 8) and control pigs (T1)

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL18045

79 Samples

Download data: TXT

(Submitter supplied) Colon cancer is a major cause of cancer deaths in Western countries and is associated with diets high in red meat. Heme, the iron-porphyrin pigment of red meat, induces cytotoxicity of gut contents which injures surface cells leading to compensatory hyperproliferation of crypt cells. This hyperproliferation results in epithelial hyperplasia which increases the risk of colon cancer. In humans, a high red-meat diet increases Bacteroides spp in feces. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

8 Samples

Download data: CEL

(Submitter supplied) Previously, we showed that dietary heme injured the colonic surface epithelium and induced hyperproliferation by changing the surface to crypt signaling. In this study we investigated whether bacteria play a role in this changed signaling. Dietary heme increased the Bacteroidetes and decreased the Firmicutes in colonic content. This shift was caused by a selective susceptibility of Gram-positive bacteria to the heme cytotoxic fecal waters, which is not observed for Gram-negative bacteria allowing expansion of the Gram-negative community. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

2 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6246 GPL1261

20 Samples

Download data: CEL

(Submitter supplied) The risk for colon cancer is associated with nutrition, especially high fat and low calcium diets high in red meat. Red meat contains the iron porphyrin pigment heme, which induces cytotoxicity of the colon contents and epithelial hyperproliferation. Using a mouse model, we showed that heme caused damage to the colonic surface epithelium and induced compensatory hyperproliferation. Expression levels of heme- and stress-related genes show that heme affects surface cells and not directly crypt cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

16 Samples

Download data: CEL

(Submitter supplied) The risk for colon cancer is associated with nutrition, especially with diets high in red meat. Red meat contains the iron porphyrin pigment heme, which induces cytotoxicity of the colon contents and epithelial hyperproliferation. Using a mouse model, we showed that heme caused damage to the colonic surface epithelium and induced compensatory hyperproliferation. Expression levels of heme- and stress-related genes show that heme affects surface cells and not directly crypt cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

4 Samples

Download data: CEL

(Submitter supplied) In this RNA-Seq dataset, we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA-Seq data revealed starvation-induced alterations in transcript levels for many genes, including a decrease in lipid metabolism and an increase in innate immune responses. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

23 Samples

Download data: TXT

(Submitter supplied) The host genotype has been proposed to contribute to individually composed bacterial communities in the gut. To provide deeper insight into interactions between gut bacteria and their host, we associated germ-free C3H and C57BL/10 mice with intestinal bacteria from a C57BL/10 donor mouse. Analysis of microbiota similarity between the experimental animals with denaturing gradient gel electrophoresis (DGGE) 13 weeks after association revealed the development of a mouse strain specific microbiota. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16983

23 Samples

Download data: CEL

(Submitter supplied) The gut-uterus axis plays a pivotal role in the pathogenesis of endometrial cancer (EC). However, the correlations between the endometrial microbiome and endometrial tumor transcriptome in patients with EC and the impact of the endometrial microbiota on hematological indicators have not been thoroughly clarified. In this prospective study, endometrial tissue samples collected from EC patients (n = 30) and healthy volunteers (n = 10) were subjected to 16S rRNA sequencing of the microbiome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

60 Samples

Download data: XLS

(Submitter supplied) Using a systems biology approach, we discovered and dissected a three-way interaction between the immune system, the intestinal epithelium, and the microbiota. We found that mice lacking B lymphocytes, or lacking IgA, have low intestinal expression of lipid metabolism genes regulated by the transcription factor GATA4, and a consequent decrease in fat absorption in the intestine. The defect disappeared in germ free mice, suggesting that it is dependent on the microbiota; and sequencing analysis of the bacteria showed subtle differences between normal and B-cell deficient mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL14915

12 Samples

Download data: TXT

(Submitter supplied) Using a systems biology approach, we discovered and dissected a three-way interaction between the immune system, the intestinal epithelium, and the microbiota. We found that mice lacking B lymphocytes, or lacking IgA, have low intestinal expression of lipid metabolism genes regulated by the transcription factor GATA4, and a consequent decrease in fat absorption in the intestine. The defect disappeared in germ free mice, suggesting that it is dependent on the microbiota; and sequencing analysis of the bacteria showed subtle differences between normal and B-cell deficient mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL14915

20 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6480 GPL14915 GPL6806

138 Samples

Download data: TXT

(Submitter supplied) Using a systems biology approach, we discovered and dissected a three-way interaction between the immune system, the intestinal epithelium, and the microbiota. We found that mice lacking B lymphocytes, or lacking IgA, have low intestinal expression of lipid metabolism genes regulated by the transcription factor GATA4, and a consequent decrease in fat absorption in the intestine. The defect disappeared in germ free mice, suggesting that it is dependent on the microbiota; and sequencing analysis of the bacteria showed subtle differences between normal and B-cell deficient mice. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

6 Samples

Download data: TXT