The production of functional mRNA involves multiple steps including transcription initiation, elongation, and termination. spt5 encodes a conserved essential transcription elongation factor that controls RNAPII processivity in vitro and co-localizes with RNAPII in vivo.
Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo.
No sample metadata fields
View SamplesTo assess the potential of PP6 as a therapeutic target in liver disorders, we attenuated expression of the PP6 catalytic subunit in HepG2 cells using lentiviral-transduced shRNA. Two PP6 knock-down (PP6KD) cell lines 18.5 and 19.5, (90% reduction of PP6-C protein content) were studied in depth.
Adaptation of HepG2 cells to a steady-state reduction in the content of protein phosphatase 6 (PP6) catalytic subunit.
Specimen part, Cell line, Treatment
View SamplesModels for tumorigenesis can be made by transforming normal cells with defined genetic elements. This allows us to determine that adrenocortical tumor development and progression follows a multistep model. Morever, we demonstrated that the order of genetic events has a great consequence on the phenotype of the resultant tumor. We performed transcriptomic analysis using cDNA microarrays to identify the molecular signature that might explain the distinctive in vivo phenotypes observed in response to both orders of the mutational events.
Acquisition order of Ras and p53 gene alterations defines distinct adrenocortical tumor phenotypes.
Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation.
No sample metadata fields
View SamplesMemory T cells are primed for rapid responses to antigen; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpG) mapped by deep sequencing to T cell activation in human nave and memory CD4 T cells. 466 CpGs (132 genes) displayed differential methylation between nave and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in memory cells coupled with increased gene expression with activation compared to nave cells, revealing specific genes more rapidly expressed in memory compared to nave cells and potentially regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression.
Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation.
No sample metadata fields
View SamplesMemory T cells are primed for rapid responses to antigen; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpG) mapped by deep sequencing to T cell activation in human naïve and memory CD4 T cells. 466 CpGs (132 genes) displayed differential methylation between naïve and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in memory cells coupled with increased gene expression with activation compared to naïve cells, revealing specific genes more rapidly expressed in memory compared to naïve cells and potentially regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression. Overall design: RNA sequencing of primary human naïve and memory CD4 T cells at rest and 48 hours post-activation.
Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation.
No sample metadata fields
View SamplesIllumina sequencing was used to assay the effect of mifepristone treatment on gene expression in adult Drosophila, including males, virgin females and mated females. Overall design: Males of strain w[1118]; p53B[6] were crossed to virgins of w[1118]; rtTA(3)E2 and progeny males and virgins were collected over 48 hours. One half of the virgins were mated to w[1118] males at ratio of 1:1 virgins to males for 4 days. Mated females were then separated from the w[1118] males. The mated females, males and virgins females were then maintained at approximately 20 flies per vial, on food with and without supplementation with 160ug/ml mifepristone for 12 days. Total fly RNA was isolated from 20 animals per sample. Three replicate samples were generated for each type of flies: males, mated females and virgin females.
The progesterone antagonist mifepristone/RU486 blocks the negative effect on life span caused by mating in female Drosophila.
Specimen part, Subject
View SamplesUp to now the role of tumor-specific pTregs and anergic cells during tumor development is not fully understood. Here we used a genetically-induced tumor expressing a MHC-II restricted DBY model antigen to characterize the tumor-induced pTregs and anergic cells that arise early during tumor development.
Induction of anergic or regulatory tumor-specific CD4<sup>+</sup> T cells in the tumor-draining lymph node.
Time
View SamplesUp to know CD4 T cell antitumor responses have been mostly studied in transplanted tumor models. However, although they are valuable tools, they are not suitable to study the long term interactions between tumors and the immune system
Induction of anergic or regulatory tumor-specific CD4<sup>+</sup> T cells in the tumor-draining lymph node.
Time
View SamplesCD4+ T cells as mediators of antitumor responses are beginning to be appreciated. Our team demonstrated that chronically activated CD4+ T cells (chCD4+ T cells) were expanded in the blood of cancer patients and their expansion is correlated with tumor regression.
Induction of anergic or regulatory tumor-specific CD4<sup>+</sup> T cells in the tumor-draining lymph node.
Disease
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