GEO DataSets

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) 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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(Submitter supplied) d-serine is naturally present throughout the human body. It is also used as add-on therapy for treatment-refractory schizophrenia. d-Serine interacts with the strychnine-insensitive glycine binding site of NMDA receptor, and this interaction could lead to potentially toxic activity (i.e., excitotoxicity) in brain tissue. The transcriptomic changes that occur in the brain after d-serine exposure have not been fully explored. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3643

Platform:

GPL1355

24 Samples

Download data: CEL

Analysis of forebrains of animals treated with up to 500 mg/kg D-serine for 96 hours. D-serine is involved in many physiological processes through its interaction with the glycine binding site of the NMDA receptor. Results provide insight into the impact of D-serine exposure on neuronal functions.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 agent, 6 dose sets

Platform:

GPL1355

Series:

GSE10748

24 Samples

Download data: CEL

(Submitter supplied) Work with pathogens like Vibrio cholerae has shown major differences between gene expression in bacteria grown in vitro and in vivo. To explore this subject for commensals, we investigated the transcription of the Lactobacillus johnsonii NCC533 genome during in vitro using the microarray technology. In broth growth, 537, 626 and 277 of the 1756 tested genes were expressed during exponential, “adaptation” (early stationary phase) and stationary phase, respectively. more...

Organism:

Lactobacillus johnsonii; Lactobacillus johnsonii NCC 533

Type:

Expression profiling by array

Platform:

GPL5958

18 Samples

Download data: TXT

(Submitter supplied) Whole tissues corresponding to the proximal and distal small intestine and to the colon were dissected from each rat, washed with ice-cold saline solution and immediately frozen in liquid nitrogen. Rats were either control or treated with Amoxicillin (100mg/kg/day). Small intestine was divided in two identical length considered as the proximal and distal part. In each intestinal part 1 cm of tissue was taken in the middle of this part to perform the RNA extraction and then the GeneArray analysis. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS1273

Platform:

GPL341

35 Samples

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Analysis of small intestine and colon of Sprague-Dawleys treated with 100 mg/kg/day of amoxicillin from 7 days of age until day 17 or day 21. Results provide insight into the effect of antibiotics on gut barrier function maturation.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 agent, 2 time, 3 tissue sets

Platform:

GPL341

Series:

GSE2354

35 Samples

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(Submitter supplied) Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by co-culture with the oral pathogenic Porphyromonas gingivalis and Aggregatibacter (formerly actinobacillus) actinomycetemcomitans. We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3211

Platform:

GPL96

12 Samples

Download data: CEL

Analysis of gingival epithelial HIGK cells infected with Aggregatibacter actinomycetemcomitans or Porphyromonas gingivalis. A. actinomycetemcomitans and P. gingivalis cause periodontal infections. Results provide insight into differences in epithelial cell responses to these pathogens.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 infection sets

Platform:

GPL96

Series:

GSE9723

12 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling with microarrays was used to identify genes differentially expressed in the lungs of B6 and BALB CF mice compared to non-CF littermates Keywords: disease state analysis

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1941

Platform:

GPL1261

23 Samples

Download data: CEL

Analysis of lungs of C57BL/6J (B6) or BALB/c (BALB) animals deficient for cystic fibrosis transmembrane conductance regulator (CFTR). B6 background animals have a higher propensity to develop CF lung disease. Results suggest the variable severity of CF is controlled by multiple genetic factors.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 gender, 2 genotype/variation, 2 strain sets

Platform:

GPL1261

Series:

GSE3100

23 Samples

Download data: CEL

(Submitter supplied) Studies using mice with beta4 nicotinic acetylcholine receptor (nAChR) subunit deficiency (beta4-/- mice) helped reveal the roles of this subunit in bradycardiac response to vagal stimulation, nicotine-induced seizure activity and anxiety. In order to identify genes that might be related to beta4-containing nAChRs activity, we compared the mRNA expression profiles of brains from beta4-/- and wild-type mice using Affymetrix U74Avr2 microarray. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2309

Platform:

GPL81

11 Samples

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Analysis of brains of beta-4 nicotinic acetylcholine receptor (nAChR) subunit null mutants. nAChRs are pentameric ion channels. Results provide insight into the molecular basis of the beta-4 subunit's role in the bradycardic response to vagal stimulation, nicotine-induced seizure, and anxiety.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL81

Series:

GSE5320

11 Samples

Download data

(Submitter supplied) Background: The skin harbors complex communities of resident microorganisms, yet little is known of their physiological roles and the molecular mechanisms that mediate cutaneous host-microbe interactions. Here, we profiled skin transcriptomes of mice reared in the presence and absence of microbiota to elucidate the range of pathways and functions modulated in the skin by the microbiota. Results: A total of 2820 genes were differentially regulated in response to microbial colonization and were enriched in gene ontology (GO) terms related to the host-immune response and epidermal differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

16 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) 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) We compared gene expression in the small intestine (ileum) of mice that were either (i) germ-free, (ii) colonized with a conventional mouse cecal microbiota, (iii) colonized with a conventional zebrafish gut microbiota, or (iv) colonized with Pseudomonas aeruginosa PAO1. Keywords: response to microbial colonization

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

18 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

100 Samples

Download data: CEL