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Homo sapiens
68 Downloadable Samples
Affymetrix Human X3P Array (u133x3p), Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 38 Downloadable Samples
Affymetrix Human X3P Array (u133x3p), Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
We used gene expression profiling of human DCIS and IBC to discover uniquely expressed genes that may also regulate progression.
Publication Title
Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2), Affymetrix Human X3P Array (u133x3p)
Description
We used gene expression profiling of human DCIS and IBC to discover uniquely expressed genes that may also regulate progression.
Publication Title
Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 13 Downloadable Samples
- Affymetrix Human X3P Array (u133x3p), Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
We used gene expression profiling of human DCIS and IBC to discover uniquely expressed genes that may also regulate progression.
Publication Title
Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Mus musculus
- 111 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Mice fed rapamycin have an increase in lifespan associated with major changes in the liver transcriptome.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Mus musculus, Helicobacter pylori
- 60 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 69 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Analysis of the effect of gene expression in the livers of old mice (25 months of age) fed rapamycin chronically (21 months) from 4 months of age.
Publication Title
Mice fed rapamycin have an increase in lifespan associated with major changes in the liver transcriptome.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Mus musculus
- 60 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Helicobacter pylori infection is associated with development of gastric adenocarcinoma in a subset of infected humans, especially those that develop an antecedent condition, chronic atrophic gastritis (ChAG) characterized by loss of acid-producing parietal cells. Studies in a gnotobiotic transgenic mouse model of ChAG, with an engineered ablation of parietal cells and an associated expansion of gastric epithelial progenitors (GEPs), have shown that a subset of GEPs is able to harbor intracellular collections of H. pylori. To better understand H. pyloris adaptation to ChAG, we sequenced the genomes of 24 isolates, obtained from 6 individuals, each sampled over a 4-year interval, as they maintained normal gastric histology, or progressed from normal histology to ChAG, or experienced worsening ChAG, or proceeded from ChAG to cancer. Analyses of gene content and single nucleotide polymorphisms (SNPs) demonstrated that H. pylori populations within study participants were largely clonal, and remarkably stable over the 4-year interval, regardless of disease state. Because they exhibited such broad inter-host variation (38.64.7 SNPs/1000bp of genome), and did not cluster according to host pathology, we sought to identify common functional properties by performing GeneChip studies of the responses of a cultured mouse gastric stem cell-like line (mGEPs) to infection with sequenced strains. The results yielded a shared 695-member set of genes differentially expressed after infection with ChAG-associated, but not normal or heat killed strains: 434 of these genes were also represented in dataset of responses to the cancer-associated strain. Ingenuity Pathway Analysis revealed that ChAG- and ChAG/cancer- associated responses were significantly enriched in genes associated with tumorigenesis in general, and gastric carcinogenesis in specific cases. Whole genome transcriptional profiling of a sequenced ChAG strain during mGEP infection disclosed a set of responses that included upregulation of hopZ, an adhesin belonging to a family of outer membrane proteins. Expression profiles of wild-type and hopZ strains revealed a number of pH-regulated genes affected by loss of HopZ, including HopP which binds sialylated glycans produced by GEPs in vivo. Genetic inactivation of hopZ produces a fitness defect in gnotobiotic transgenic mice but not their wild-type littermates. This study illustrates an approach for identifying GEP responses specific to ChAG, and bacterial genes important for survival in a gastric ecosystem that lacks parietal cells.
Publication Title
Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples
GSE12838- Homo sapiens
- 56 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
INTRO: The ongoing challenge of accurately diagnosing infection in the ICU motivates a search for novel molecular diagnostics. In the current study, we tested the hypothesis that the informational content of circulating leukocytes differs, thereby allowing one to rank leukocyte populations on their potential to contribute to RNA diagnostics for pneumonia.
Publication Title
No associated publication
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 54 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Using anti-Argonaute (anti-AGO) antibody co-immunoprecipitation, followed by microarray analyses and downstream bioinformatics, RIP-Chip experiments enable direct analyses of miRNA targets. The analyses support four major findings: (i) RIP-Chip studies correlated with total input mRNA profiling provides more comprehensive information than using either RIP-Chip or total mRNA profiling alone after miRNA transfections; (ii) new data confirm that miR-107 paralogs target coding sequence (CDS) of mRNA; (iii) biochemical and computational studies indicate that the 3 portion of miRNAs plays a role in guiding miR-103/7 to the CDS of targets; and (iv) there are major sequence-specific targeting differences between miRNAs in terms of CDS versus 3-untranslated region targeting, and stable AGO association versus mRNA knockdown. For detailed protocol and for full discussion of the results please see Nelson PT et al, Nucleic Acids Res. 2011 Oct;39(18):8163-72.
Publication Title
Specific sequence determinants of miR-15/107 microRNA gene group targets.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples