GEO DataSets

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) 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

(Submitter supplied) In order to test the development of gastrointestinal tract (GIT) in pre-weaned cavles, the GIT tissues were collected from day 0, day 7, day 21 and day 42 calves. RNA-seq was used to measure the transcriptome profiles. The RNA-seq analysis revealed the fast development of small intestine and rumen tissue during the first week after birth.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15749

71 Samples

Download data: TXT

(Submitter supplied) Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS640

Platform:

GPL81

24 Samples

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Analysis of germ-free and conventional corpus, jejunum, descending colon and rectum. Findings identify important interaction between commensal microbiota and gastrointestinal tract transcriptome.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 other, 4 tissue sets

Platform:

GPL81

Series:

GSE1392

24 Samples

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(Submitter supplied) Maintenance of intestinal homeostasis requires a healthy relationship between the commensal gut microbiota and the host immune system. Breast milk supplies the first source of antigen-specific immune protection in the gastrointestinal tract of suckling mammals, in the form of secretory immunoglobulin A (SIgA). SIgA is transported across glandular and mucosal epithelial cells into external secretions by the polymeric immunoglobulin receptor (pIgR). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

16 Samples

Download data: CEL

(Submitter supplied) Whole-transcriptome survey of gene expression differences between germ-free (GF) and conventionally raised (CONV-R) mice. To assess the role of toll-like receptor signalling, both wild-type and Myd88 -/- mice were used.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

77 Samples

Download data: CEL, CHP

(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) Diminished colonic health is associated with various age-related pathologies. In this study, we applied an integrative approach to reveal potential interactions between determinants of colonic health in aging C57BL/6J mice. Analysis of gut microbiota composition revealed an enrichment of various potential pathobionts, including Desulfovibrio spp., and a decline of the health-promoting Akkermansia spp. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

26 Samples

Download data: CEL

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

Organism:

Mus musculus; mouse gut metagenome

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL21051 GPL17021

60 Samples

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(Submitter supplied) Microbial functions in the host physiology are a result of co-evolution between microbial communities and their hosts. Here we show that cold exposure leads to marked shift of the microbiota composition, referred to as cold microbiota. Transplantation of the cold microbiota to germ-free mice is sufficient to increase the insulin sensitivity of the host, and enable complete tolerance to cold partly by promoting the white fat browning, leading to increased energy expenditure and fat loss. more...

Organism:

mouse gut metagenome

Type:

Other

Platform:

GPL21051

48 Samples

Download data: XLSX

(Submitter supplied) Microbial functions in the host physiology are a result of co-evolution between microbial communities and their hosts. Here we show that cold exposure leads to marked shift of the microbiota composition, referred to as cold microbiota. Transplantation of the cold microbiota to germ-free mice is sufficient to increase the insulin sensitivity of the host, and enable complete tolerance to cold partly by promoting the white fat browning, leading to increased energy expenditure and fat loss. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: XLSX

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

100 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

46 Samples

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(Submitter supplied) The highly characterized Sox9-EGFP transgenic mouse model, which permits the isolation and analysis of four distinct IEC populations using fluorescence-activated cell sorting (FACS) based on differing levels of cellular EGFP intensity. These are Sox9-EGFP Low (actively cycling IESCs), Sox9-EGFP Sublow (progenitor cells), Sox9-EGFP Neg (mostly differentiated enterocytes as well as goblet cells and Paneth cells), and Sox9-EGFP High (primarily EECs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: CSV

(Submitter supplied) We evaluated miRNA expression profiles by next-generation high-throughput small RNA-sequencing in distinct IEC subtypes of germ-free (GF) and conventionalized (CV) mice. We used the highly characterized Sox9-EGFP transgenic mouse model, which permits the isolation and analysis of four distinct IEC populations using fluorescence-activated cell sorting (FACS) based on differing levels of cellular EGFP intensity. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

56 Samples

Download data: CSV

(Submitter supplied) Consumption of diets rich in fibers has been associated with several beneficial effects on gastrointestinal health. However, detailed studies on the molecular effects of fibers in colon are limited. In this study we investigated and compared the influence of five different fibers on the mucosal transcriptome, and luminal microbiota and SCFA concentrations in murine colon. Mice were fed diets enriched with fibers that differed in carbohydrate composition, namely inulin (IN), oligofructose (FOS), arabinoxylan (AX), guar gum (GG), resistant starch (RS) or a control diet (corn starch) for 10 days. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

35 Samples

Download data: CEL

(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) Laser captured cecal epithelium from gnotobiotic mice colonized with B. thetaiotaomicron or B. longum (mono-association) or B. thetaiotaomicron bi-association with B. longum. Samples were derived from 10d colonizations of NMRI mice fed a standard-chow polysaccharide rich (PR) diet. Keywords: Germ-free vs. Mono-associations or Bi-association, in vivo

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL1981 GPL1261

16 Samples

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

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

34 Samples

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