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GSE42021
Mus musculus
27 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We investigated at which stage of maturation commitment to a stable Foxp3-expressing phenotype takes place. We assessed stability of Foxp3 expression in thymic Foxp3+ Treg subsets of different maturity, defined by CD24 expression. Next we compared gene expression profiles of Foxp3+ Treg subsets (+) of different maturity (24lo, 24int, 24hi) and could identify a set of genes that were specifically up or downregulated in Foxp3+ Tregs, but not in Foxp3- conventional T cells, in a maturation-dependent manner.
Publication Title
Active demethylation of the Foxp3 locus leads to the generation of stable regulatory T cells within the thymus.
Sample Metadata Fields
Specimen part
View Samples- Pseudomonas aeruginosa
- 4 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
At mid-log phase (OD600 of 0.5), unique gene expression patterns were observed between these two strains with 3.4% of the transcripts (188/5570) expressed differentially.
Publication Title
A novel oxidized low-density lipoprotein-binding protein from Pseudomonas aeruginosa.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 88 Downloadable Samples
Illumina HiSeq 2000
Description
Through Next Generation Sequencing (mRNA-Seq) of intracellular miRNAs in measles virus-stimulated B and CD4+ T cells isolated from high and low antibody responders to measles vaccination, we identified a set of B cell-specific miRNAs (e.g., miR-151a-5p, miR-223, miR-29, miR-15a-5p, miR-199a-3p, miR-103a, and miR-15a/16 cluster) associated with measles-specific antibody response after vaccination. No CD4+ T cell-specific miRNA expression differences between high and low antibody responders were found. DIANA tool was used for gene/target prediction and pathway enrichment analysis and this yielded several biological processes/pathways, including regulation of adherens junction proteins, Fc-receptor signaling pathway, phosphatidylinositol-mediated signaling pathway, growth factor signaling pathway/pathways, transcriptional regulation, apoptosis and virus-related processes, that were significantly associated with neutralizing antibody titers after measles vaccination. This study demonstrates that miRNA expression directly or indirectly influences humoral immunity to measles vaccination and suggests that B cell-specific miRNAs may potentially serve as predictive biomarkers of vaccine response. Overall design: Examination of miRNA expression differences in/between purified B and CD4+ T cells of high and low responders to measles vaccination.
Publication Title
Differential miRNA expression in B cells is associated with inter-individual differences in humoral immune response to measles vaccination.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 40 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Activated B-cell-like (ABC) and germinal center B-cell-like (GCB) diffuse large B-cell lymphoma (DLBCL) represent the two major molecular DLBCL subtypes. They are characterized by differences in clinical course and by divergent addiction to oncogenic pathways. To determine activity of novel compounds in these two subtypes, we conducted an unbiased pharmacologic in vitro screen. The phosphatidylinositol-3-kinase (PI3K) alpha/delta (PI3Ka/d) inhibitor AZD8835 showed marked potency in ABC DLBCL models, whereas the protein kinase B (AKT) inhibitor AZD5363 induced apoptosis in PTEN-deficient DLBCLs. These in vitro results were confirmed in various cell line xenograft and patient-derived xenograft mouse models in vivo. Treatment with AZD8835 induced inhibition of nuclear factor kappa-B (NF-kB) signaling, prompting us to combine AZD8835 with the Brutons tyrosine kinase (BTK) inhibitor ibrutinib. This combination was highly synergistic and effective both in vitro and in vivo. In contrast, the AKT inhibitor AZD5363 was effective in PTEN-deficient DLBCLs through downregulation of the oncogenic transcription factor MYC. Collectively our data suggest that patients should be stratified according to their oncogenic dependencies when treated with PI3K and AKT inhibitors.
Publication Title
Sensitivity to PI3K and AKT inhibitors is mediated by divergent molecular mechanisms in subtypes of DLBCL.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Conjugates of fatty acids and amines, including endocannabinoids, are known to play important roles as endogenous signalling molecules. Among these, the ethanolamine conjugate of the n-3 poly unsaturated long chain fatty acid (PUFA) docosahexaenoic acid (22:6n-3) (DHA) was shown to possess strong anti-inflammatory properties.
Publication Title
Docosahexaenoyl serotonin, an endogenously formed n-3 fatty acid-serotonin conjugate has anti-inflammatory properties by attenuating IL-23-IL-17 signaling in macrophages.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 26 Downloadable Samples
- Illumina HiSeq 2000
Description
Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in the U.S. annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). In order to identify potential targets for molecularly targeted chemoprevention, we performed integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar UV-driven Hairless mouse model. We identified the major transcriptional drivers of this sequence showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this UV-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible. Overall design: We sought to identify important genetic events that drive squamous cell carcinoma development through combined analysis of next generation sequencing of matched patient samples with a UV-driven mouse model to identify key pathways.
Publication Title
Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HumanWG-6 v3.0 expression beadchip
Description
Two independent induced pluripotent stem cell lines: ES4CL1 (derived from foreskin) and MR90C2 (derived from lung Fibroblast) were maintained on inactivated mouse embryonic fibroblast (MEF) feeder cells in the presence of ESC media containing DMEM, 20% knock-out serum replacement with 100ng/mL of bFGF. 7 days after seeding, cells were harvested in TrypLE Express and FACs sorted using antibodies detecting the presence of cell surface antigens GCTM-2 and CD9.
Publication Title
Identification of unsafe human induced pluripotent stem cell lines using a robust surrogate assay for pluripotency.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Several aspects common to a Western lifestyle, including obesity and decreased physical activity, are known risks for gastrointestinal cancers. There is an increasing amount of evidence suggesting that diet profoundly affects the composition of the intestinal microbiota. Moreover, there is now unequivocal evidence linking a dysbiotic gut to cancer development. Yet, the mechanisms through which high-fat diet (HFD)-mediated changes in the microbial community impact the severity of tumorigenesis in the gut, remain to be determined.
Publication Title
High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
Canonical WNT-signaling is essential for placode formation irrespective of appendage type. At sites of placode initiation, Although WNT-signaling occurs in both epithelium and mesenchyme, the site of most intense activity as revealed by the WNT reporter Axin2-LacZ was in a zone just below the epithelial-mesenchymal interface. In ventral foot-skin, this WNT activity peaked at E17.5, concomitant with sweat bud fate commitment, while in dorsal back-skin, it began at E14.5, concomitant with HF fate specification. Overall design: To address whether WNT-signaling within this zone might regionally influence the transcriptional landscape of body-site mesenchymes to support distinct epithelial fates, we transcriptionally profiled the Axin2-positive and Axin2-negative dermal cells following their FACS-purification from E17.5 ventral foot-skin and E14.5 dorsal back-skin
Publication Title
Spatiotemporal antagonism in mesenchymal-epithelial signaling in sweat versus hair fate decision.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Specific microRNAs are preferentially expressed by skin stem cells to balance self-renewal and early lineage commitment.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples