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GSE93664
Homo sapiens
3 Downloadable Samples
Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Pathogen-specific polyfunctional T cell responses have been associated with favorable clinical outcomes but it is not known whether polyfunctional T cells are distinct from monofunctional cytokine producing T cells. In this study we compared the transcriptomic profile of P. falciparum reactive polyfunctional and IFNg monofunctional CD4 T cells by microarray analysis and show that polyfunctional CD4 T cells are associated with a unique transcriptomic signature.
Publication Title
Polyfunctional and IFN-<b>γ</b> monofunctional human CD4<sup>+</sup> T cell populations are molecularly distinct.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
HNF4alpha is a master regulator of hepatic differentiation. In this study, HNF4alpha was deleted in adult mice using a Cre-LoxP system where Cre recombinase was delivered using an AAV8 virus.
Publication Title
Hepatocyte-specific deletion of hepatocyte nuclear factor-4α in adult mice results in increased hepatocyte proliferation.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Liver undergoes both size increase and differentiation during postnatal period, which in mice is approximately first 30 days. The mechanisms of simultaneous postnatal liver cell proliferation and maturation are not clear. In these experiments, role of yes associated protein (Yap), the downstream effector of Hippo Kinase signaling pathway was investigated.
Publication Title
Yes-associated protein is involved in proliferation and differentiation during postnatal liver development.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 9 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Activated pancreatic stellate cells produce the fibrotic matrix in chronic pancreatitis and pancreatic cancer. In vitro protocols examining PSC biology have usually involved PSCs cultured on plastic, a non-physiological surface. However, PSCs cultured on physiological matrices e.g. MatrigelTM (normal basement membrane) and collagen (fibrotic pancreas), may have distinctly different behaviours compared to cells cultured on plastic. Therefore, we aimed to compare PSC gene expression after culture on plastic, MatrigelTM and collagen I.
Publication Title
Extracellular matrix composition significantly influences pancreatic stellate cell gene expression pattern: role of transgelin in PSC function.
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Microarray analysis on total retinal RNA from 15 day old Sirt6 wild-type (WT) and knock-out (KO) mice.
Publication Title
SIRT6 is required for normal retinal function.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Macrophage aging is pathogenic in numerous diseases, including age-related macular degeneration. Although prior studies have explored the functional consequences of macrophage aging, less is known about its cellular basis or what defines the transition from physiologic aging to disease. The purpose of this experiment was to characterize the transcriptomic changes associated with macrophage aging.
Publication Title
Oxysterol Signatures Distinguish Age-Related Macular Degeneration from Physiologic Aging.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Mice were fed with either normal diet (ND), 0.2% cholic acid diet (0.2%CA), DEN treated and fed ND or DEN treated and fed 0.2%CA diet. DEN was treated at 15 microgram/kg body weight at postnatal day 15. Diets were fed for two months starting 8 months of age till 10 months of age. Livers were collected at10 months of age, Total RNA was isolated and used for microarray experiments.
Publication Title
Bile acids promote diethylnitrosamine-induced hepatocellular carcinoma via increased inflammatory signaling.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Estrogens and progesterone control mammary gland development and breast carcinogenesis via their cognate receptors expressed in a subset of cells of the luminal layer of the mammary epithelium. The extracellular matrix (ECM) including the basement membrane (BM) is important in breast physiology and tumorigenesis but how epithelial hormone receptor signaling and ECM are linked mechanistically is unclear. We identify the secreted protease Adamts18 as critical intermediary. Luminal estrogen and progesterone receptor signaling via upregulation of Wnt4 expression and ensuing canonical Wnt signaling activation in basal cells control Adamts18 expression there. The protease has an epithelial-intrinsic role in stem cell activation. We identify multiple binding partners in the interstitial ECM and BM and show that ADAMTS18 cleaves fibronectin in vitro. Its deletion results in increased fibronectin, collagen I and IV, and laminin deposition in pubertal glands. Adamts18 interacts genetically with Col18a1, which encodes a proteoglycan that is BM-specific, in stem cell regulation. Adamts18 inactivation impairs Hippo signaling and reduces Fgfr2 expression and signaling, which are vital for stem cell function. Our findings link epithelial hormone signaling to BM remodeling by Adamts18, and define the BM as an essential stem cell niche component.
Publication Title
The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
Illumina HiSeq 2500
Description
Dysfunctional mitochondria and generation of reactive oxygen species (ROS) promote chronic diseases, which have spurred interest in the molecular mechanisms underlying these conditions. Previously, we have demonstrated that disruption of post-translational modification of proteins with ß-linked N-acetylglucosamine (O- glcnAcylation) via overexpression of the O-glcnAc–regulating enzymes O- glcnAc transferase (OGT) or O- glcnAcase (OGA) impairs mitochondrial function. Here, we report that sustained alterations in O- glcnAcylation either by pharmacological or genetic manipulation also alters metabolic function. Sustained O-glcnAc elevation in SH-SY5Y neuroblastoma cells increased OGA expression and reduced cellular respiration and ROS generation. Cells with elevated O-glcnAc levels had elongated mitochondria and increased mitochondrial membrane potential, and RNA-Seq in SH-SY5Y cells indicated transcriptome reprogramming and down regulation of the NRF2-mediated antioxidant response. Sustained O-glcnAcylation in mice brain and liver validated the metabolic phenotypes observed in the cells, and OGT knockdown in the liver elevated ROS levels, impaired respiration, and increased the NRF2 antioxidant response. Moreover, elevated O-glcnAc levels promoted weight loss and lowered respiration in mice and skewed the mice toward carbohydrate-dependent metabolism as determined by indirect calorimetry. In summary, sustained elevation in O-glcnAcylation coupled with increased OGA expression reprograms energy metabolism, a finding that has potential implications for the etiology, development, and management of metabolic diseases. Overall design: SY5Y cells were adapted to long term O-glcnAcase (OGA) inhibition using the specific OGA inhibitor Thiamet-G (tmg) or glucosamine treatment for 3 weeks. After adaptation to the growth conditions, cells were harvest and RNA isolated for Next Generation RNA sequencing. Briefly, cDNA library was prepared using Illumina TruSeq Stranded mRNA sample preparation kit (Illumina) as manufacturer's instruction. Total RNA was isolated using the same method as previously described and 800 ng of the total RNA per reaction was used to initiate the protocol. The quality of RNA sequencing results was first assessed using FastQC (0.11.2). RSEM (1.2.22) was utilized to align the reads to the human reference genome HG38 and to calculate gene expression values. EdgeR (3.14.0) was then used to normalize the expression values using the TMM-method (weighted trimmed mean of M-values), and for differential expression analyses. First, the negative binomial conditional common likelihood was maximized to estimate a common dispersion value across all genes (estimateCommonDisp). Next, tagwise dispersion values were estimated by an empirical Bayes method based on weighted conditional maximum likelihood (estimateTagwiseDisp). Finally, the differentially gene expression was calculated by computing genewise exact tests for differences in the means between two groups of negative-binomially distributed counts. Hierarchical clustering analysis was determined using Euclidean distance. The following R-packages were utilized for calculations and visualizations: plots and edgeR.
Publication Title
Sustained <i>O-</i>GlcNAcylation reprograms mitochondrial function to regulate energy metabolism.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 59 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
BAD phosphorylation determines ovarian cancer chemosensitivity and patient survival.
Sample Metadata Fields
Disease stage, Cell line
View Samples