To identify proteins regulated by glucose through changes in their rate of protein synthesis, translational profiling of MIN6 cells acutely incubated at either low or high glucose concentration was performed (i.e. microarray analysis was performed on mRNAs associated with polysomes, as an increase in the association of mRNA with polysomes is indicative of an increase in the rate of initiation step of translation and hence an increase in protein expression) (Johannes et al., 1999; Mikulits et al., 2000).
Distinct glucose-dependent stress responses revealed by translational profiling in pancreatic beta-cells.
Specimen part, Cell line, Compound, Time
View SamplesSympathetic hyperactivity can result from cell-autonomous changes in neurons that innervate cardiovascular target tissues. Stellate ganglia are of particular interest because the majority of sympathetic neurons innervating the heart reside there. The cardiovascular risk profiles in men and women are different. Transcriptomics provides a powerful tool for identifying genomic changes that contribute to sympathetic dysfunction in disease. Here we compared the transcriptomes of healthy stellate ganglia from adult male and female WKY rats.
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Sex, Age, Specimen part, Disease, Cell line, Treatment
View SamplesBilirubin is a potent antioxidant that reduces inflammation and the accumulation of fat. There have been reports of gene responses to bilirubin, which was mostly attributed to its antioxidant function. These RNA-sequencing studies investigated the impact biliverdin, which is rapidly reduced to bilirubin, has on transcriptome responses in human HepG2 hepatocytes in a PPARa-dependent fashion. This investigation reveals that transcriptome responses from the generation of bilirubin are mostly PPARa-dependent, and its antioxidant function regulates a smaller set of genes.
No associated publication
Sex, Age, Specimen part, Disease, Cell line, Treatment, Race
View SamplesAlterations in the tissue microenvironment collaborate with cell autonomous genetic changes to contribute to neoplastic progression. The importance of the microenvironment in neoplastic progression is underscored by studies demonstrating that fibroblasts isolated from a tumor stimulate the growth of preneoplastic and neoplastic cells in xenograft models. Similarly, senescent fibroblasts promote preneoplastic cell growth in vitro and in vivo. Because senescent cells accumulate with age, their presence is hypothesized to facilitate preneoplastic cell growth and tumor formation in older individuals. To identify senescent stromal factors directly responsible for stimulating preneoplastic cell growth, we carried out whole genome transcriptional profiling and compared senescent fibroblasts to their younger counterparts. We identified osteopontin (OPN) as one of the most highly elevated transcripts in senescent fibroblasts. Importantly, reduction of OPN protein levels by RNAi did not impact senescence induction in fibroblasts; however, it dramatically reduced the growth-promoting activities of senescent fibroblasts in vitro and in vivo, demonstrating that OPN is necessary for paracrine stimulation of preneoplastic cell growth. In addition, we found that recombinant OPN was sufficient to stimulate preneoplastic cell growth. Finally, we demonstrate that OPN is expressed in senescent stroma within preneoplastic lesions that arise following DMBA/TPA treatment of mice, suggesting that stromal-derived OPN-mediated signaling events impact neoplastic progression.
Senescent stromal-derived osteopontin promotes preneoplastic cell growth.
No sample metadata fields
View SamplesThe goal of this study was to identify transcriptomic differences in A549 lung cancer cell line following knockout of the RPA1 gene. A549 cells, and many lung tumors, carry constitutive NRF2 activation. Understanding how RPA1 modulates transcription, particularly NRF2-mediated transcription, is relevant for future cancer therapeutics.
No associated publication
Sex, Specimen part, Cell line
View SamplesThe goal of this study was to determine the role of the X-linked epigenetic mediator, O-linked N-acetylglucosamine transferase (OGT) in establishment of trophoblast-specific sex differences in gene expression and to determine if sex differences in OGT and downstream epigenetic modifications contribute to sex differences in hypothalamic gene expression and development.
No associated publication
Sex, Specimen part, Cell line, Treatment
View SamplesEffect of expression of wild type KSHV RTA or the activation domain (aa608-651) deleted version of RTA in 293T cells on gene expression profiling.
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Cell line, Time
View Samplessearch differential gene expression with ClC-3 knockdown
No associated publication
No sample metadata fields
View SamplesThe activity of different E2F constructs with respect to gene expression was measured. E2F constructs differed in degradability, and were doxycycline inducible. Different samples with the different E2F constructs, and with or without dox inductions were assayed for gene expression.
No associated publication
Sex, Specimen part, Treatment
View SamplesAnalysis of the gene signature of steatosis associated to obesity in hepatocytes of Zucker fa/fa obese rats and their controls; identifying target genes linked to steatosis progression. or Obesity and insulin resistance-associated steatosis can be a non-inflammatory condition affecting hepatocytes or progress to steatohepatitis: a condition that can result in end-stage liver disease. Although molecular events leading to accumulation of lipid droplets in the liver have been identified individually, the complexity of the condition suggested that emergent target would be uncovered by a more comprehensive examination. Then, this study was aimed at establishing a gene signature of steatosis in hepatocytes and at identifying target genes linked to steatosis progression. Using Affymetrix oligonucleotide arrays, we compared transcriptomes of hepatocytes isolated from Zucker "fa/fa" obese rats with three different age-related grades of steatosis with those of their counterpart non-steatotic cells.
A subset of dysregulated metabolic and survival genes is associated with severity of hepatic steatosis in obese Zucker rats.
Sex, Age, Specimen part, Disease, Disease stage
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