Filters
Technology
Platform
GSE20155
Saccharomyces cerevisiae
9 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
To study how the presence of PUFAs influences central cellular processes, and in order to perform lipidome, transcriptome and molecular studies we decided to use yeast as a model organism. We therefore co-expressed 12-desaturase and 6- desaturase genes from Mucor rouxii in S. cerevisiae with the objective to obtain a yeast strain that contains PUFAs, especially linoleic acid (LA, C18:29,12) and -linolenic acid (GLA, C18:36,9,12), in its membranes.
Publication Title
Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress.
Sample Metadata Fields
Time
View Samples- Mus musculus, Drosophila melanogaster
- 2 Downloadable Samples
Illumina HiSeq 2000, Drosophila Gene 1.0 ST Array (drogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Lactobacilli Modulate Epithelial Cytoprotection through the Nrf2 Pathway.
Sample Metadata Fields
Age, Specimen part
View Samples- Drosophila melanogaster
- 2 Downloadable Samples
- Drosophila Gene 1.0 ST Array (drogene10st)
Description
We report that cellular ROS enzymatically generated in response to contact with lactobacilli in both mice and Drosophila has salutary effects against exogenous insults to the intestinal epithelium via the activation of Nrf2 responsive cytoprotective genes.
Publication Title
Lactobacilli Modulate Epithelial Cytoprotection through the Nrf2 Pathway.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 477 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
Microarray Analysis of Human Whole Blood and Intestinal Biopsy Samples from a Phase 2b, Multicenter, Randomized, Double-blind, Placebo-controlled, Parallel-group Study of Ustekinumab in Crohns Disease
Publication Title
A functional genomics predictive network model identifies regulators of inflammatory bowel disease.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Treatment
View Samples- Homo sapiens
- 125 Downloadable Samples
- Illumina HiSeq 2500
Description
This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine. Overall design: Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine. The samples were collected fresh and the tissue was further processed for isolation. A representative 0.5 cm tissue fragment was isolated from the collected surgical specimen samples, flash frozen and stored at -80C. Tissue was homogenized in Trizol following the manufacturer''s protocol (Life Technologies) and RNA extraction was performed. RIN scores >7 were used for Poly A RNA-seq.
Publication Title
A functional genomics predictive network model identifies regulators of inflammatory bowel disease.
Sample Metadata Fields
Sex, Subject
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 2.0 ST Array (ragene20st)
Description
The goal of the study was to determine the effect of lentiviral- mediated overexpression of miR-495 (LV-miR-495) on the levels of gene expression in the nuclues accumbens of rats relative to control rats injected with the empty vector (LV-GFP).
Publication Title
In silico identification and in vivo validation of miR-495 as a novel regulator of motivation for cocaine that targets multiple addiction-related networks in the nucleus accumbens.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 28 Downloadable Samples
- IlluminaHiSeq2000
Description
Pharmacological inhibition of chromatin co-regulatory factors represents a clinically validated strategy to modulate oncogenic signaling through selective attenuation of gene expression. Here, we demonstrate that CBP/EP300 bromodomain inhibition preferentially abrogates the viability of multiple myeloma cell lines. Phenotypic effects are preceded by the direct transcriptional suppression of the lymphocyte-specific transcription factor IRF4 and the subsequent down-regulation of the IRF4 transcriptional program. Ectopic expression of IRF4 antagonizes the phenotypic effects of CBP/EP300 bromodomain inhibition and prevents the suppression of the IRF4 target c-MYC. These findings suggest that CBP/EP300 bromodomain inhibition represents a viable therapeutic strategy for targeting multiple myeloma and other lymphoid malignancies dependent on the IRF4 network. Overall design: Through the use of CBP/EP300 bromodomain inhibitors (CBP/EP300i), we demonstrate that MYC expression in BETi-resistant cells is dependent on CBP/EP300 bromodomains and that treatment with CBP/EP300i restores phenotypic sensitivity.
Publication Title
Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 69 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
The gut microbiota has been implicated in obesity and cardiometabolic diseases, although evidence in humans is scarce. We investigated how gut microbiota manipulation by antibiotics (7-day administration of amoxicillin, vancomycin, or placebo) affects host metabolism in 57 obese, prediabetic men. Vancomycin, but not amoxicillin, decreased bacterial diversity and reduced Firmicutes involved in short-chain fatty acid and bile acid metabolism, concomitant with altered plasma and/or fecal metabolite concentrations. Adipose tissue gene expression of oxidative pathways was upregulated by antibiotics, whereas immune-related pathways were downregulated by vancomycin. Antibiotics did not affect tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability, and adipocyte size. Importantly, energy harvest, adipocyte size, and whole-body insulin sensitivity were not altered at 8-week follow-up, despite a still considerably altered microbial composition, indicating that interference with adult microbiota by 7-day antibiotic treatment has no clinically relevant impact on metabolic health in obese humans.
Publication Title
Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Treatment, Subject, Time
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Kaposis sarcoma-associated hepesvirus (KSHV) encodes four genes with homology to human interferon regulatory factors (IRFs). One of these IRFs, the viral interferon regulatory factor 3 (vIRF-3) is expressed in latently infected PEL cells and required for their continuous proliferation. Moreover, vIRF-3 is known to be involved in modulation of the type I interferon response.
Publication Title
Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 3 inhibits gamma interferon and major histocompatibility complex class II expression.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Anopheles gambiae
- 15 Downloadable Samples
- Affymetrix Plasmodium/Anopheles Genome Array (plasmodiumanopheles)
Description
Although the basic anatomical sub-divisions of the larval mosquito gut were established several decades ago, information regarding their exact physiological roles is rather scarce. Several studies have reported differences between larval gut compartments in various morphological and physiological aspects. Unfortunately, the fragmentary and incomplete nature of this information makes it hard to establish clear links to the specific and/or unique physiological roles of each gut region.
Publication Title
A microarray-based analysis of transcriptional compartmentalization in the alimentary canal of Anopheles gambiae (Diptera: Culicidae) larvae.
Sample Metadata Fields
No sample metadata fields
View Samples