RNA-seq of Th1 and Th2 differentiated T helper cells re-stimulated with pma/ionomycin after 7 days of differentiation.
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PROVIDER: PRJEB41969 | ENA |
REPOSITORIES: ENA
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Project description:Naive CD4 T helper cells were isolated using magnetic negative selection kit from 4 weeks old Balb\c mice. The cells were activated with anti CD3/CD28 antibodies in the presence of Th1 th2 skewing cytokines and antibodies. The cells were disconnected for resting conditions after 48hours and further proliferated for 7 days in the presence of IL2 and skewing cytokines. In the 7th day the cells were collected and re-stimulated for 1hr using PMA/ionomycin and RNA was extracted for transcriptomics.
2022-03-31 | E-MTAB-9908 | biostudies-arrayexpress
Project description:T-helper cells differentiate from naïve precursors into multiple lineages, including Th1, Th2, Th17 and inducible Treg, in humans and mice. The identification of each lineage is currently determined by examination of a small number of genes encoding hallmark cytokines and/or transcription factors in both species To gain a better understanding of human T-helper cell function we have performed detailed transcriptional profiling of highly polarized Th1 and Th2 cells in both resting and activated states examining gene and miRNA expression Naïve CD4 positive T-cells were isolated from peripheral blood of three different human donors. Cells were differenitated into Th1 and Th2 cells in vitro for 28 days to achieve homogeneous cell lineages. Samples were taken at resting state or activated for 4 hours with PMA/Ionomycin.
2016-08-01 | E-GEOD-43769 | biostudies-arrayexpress
Project description:EZH2 is a polycomb protein which is able to bind DNA or RNA directly or indirectly. In this experiment, we would like to explore EZH2 RNA binding sites in a differentiation model of mouse Th1 and Th2 helper cells. We assume that EZH2 takes part in the transcription, rather than silencing, of T helper cells related transcripts.
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Project description:EZH2 rip-seq in mouse Th1 helper cells, resting and re-stimulated with pma/ionomycin
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Project description:Natural Helper cells constitute a unique lineage of Th2-cytokine producting innate lymphocytes, here we characterize the gene expression profile of non-stimulated or PMA/ionomycin-stimulated Natural Helper cells from naive C57Bl/6 mouse lungs. We used microarrays to detail the gene expression profile of stimulated and unstimulated lung Natural Helper cells in mice. Lineage(-)Sca-1(+)c-Kit(-/low)CD127(+)CD25(+) Lung Natural Helper cells were purified from naive 6-8 week old B6 mice by FACS. RNA was extracted immediately from un-stimulated Natural Helper cells after FACS. Stimulated Natural Helper cells were cultured with PMA/ionomycin for 3 days followed by RNA extraction.
2012-02-24 | E-GEOD-36057 | biostudies-arrayexpress
Project description:Natural Helper cells constitute a unique lineage of Th2-cytokine producting innate lymphocytes, here we characterize the gene expression profile of non-stimulated or PMA/ionomycin-stimulated Natural Helper cells from naive C57Bl/6 mouse lungs. We used microarrays to detail the gene expression profile of stimulated and unstimulated lung Natural Helper cells in mice.
2012-02-24 | GSE36057 | GEO
Project description:T-helper cells differentiate from naïve precursors into multiple lineages, including Th1, Th2, Th17 and inducible Treg, in humans and mice. The identification of each lineage is currently determined by examination of a small number of genes encoding hallmark cytokines and/or transcription factors in both species To gain a better understanding of human T-helper cell function we have performed detailed transcriptional profiling of highly polarized Th1 and Th2 cells in both resting and activated states examining gene and miRNA expression
2016-08-01 | GSE43769 | GEO
Project description:T helper cell subsets have unique calcium (Ca2+) signals when activated with identical stimuli. The regulation of these Ca2+ signals and their correlation to the biological function of each T cell subset remains unclear. Trpm4 is a Ca2+-activated cation channel that we found is expressed at higher levels in Th2 cells compared to Th1 cells. Inhibition of Trpm4 expression increased Ca2+ influx and oscillatory levels in Th2 cells and decreased influx and oscillations in Th1 cells. This inhibition of Trpm4 expression also significantly altered T cell cytokine production and motility. Our experiments revealed that decreasing Trpm4 levels divergently regulates nuclear localization of NFAT. Consistent with this, gene profiling did not show Trpm4 dependent transcriptional regulation and T-bet and GATA-3 levels remain identical. Thus, Trpm4 is expressed at different levels on T helper cells and plays a distinctive role in T cell function by differentially regulating Ca2+ signaling and NFAT localization. T helper cell gene expression levels when Trpm4 is inhibited by siRNA or dominant negative Trpm4 construct. The ion channel Trpm4 was inhibited in Th1 or Th2 cells using either siRNA or a dominant negative Trpm4 retrovirus and changes in gene profiles were analyzed.
2013-01-23 | E-GEOD-21996 | biostudies-arrayexpress
Project description:Helper T cells can adopt a number of different phenotypes. We performed microarray-assisted mRNA profiling on antigen-stimulated, TCR transgenic murine splenocytes that were cultured in the presence of cytokines. Transcriptome snapshots of Th cells differentiating into Th1 and Th2 phenotypes were obtained at various time-points. Principle component analysis shows that time since activation and Th skewing are the largest sources of variance (i.e., the largest contributing factors) in our profiling experiments. Divergence between the Th1 and Th2 phenotypes is established early and does not increase in terms of number of differential genes from day 1 to day 4 after stimulation. Notwithstanding the lack of further divergence between the Th1 and Th2 lineages, we show that gene expression is best described by a turnover rather than a core response model, although we find evidence for both. We identify clusters of skewed genes associated with early-persistent (core response) and late (turnover) Th1 and Th2 gene expression. In addition to the classical Th genes, members of the Batf transcription factor family are differentially expressed in particular helper phenotypes, suggesting an important role for this family in helper T-cell phenotype differentiation.
2013-03-01 | E-MTAB-1475 | biostudies-arrayexpress
Project description:CD4+ T cell differentiation is a key element of the adaptive immune system driving appropriate immune responses by selective differentiation into specialized subsets such as Th1 and Th2 cells. Besides those canonical Th cell lineages, hybrid phenotypes such as Th1/2 cells have been identified in vivo, and their generation could be reproduced in vitro. While master transcription factors like T-bet and GATA-3 regulate and maintain differentiation into the canonical lineages, the transcriptional architecture of hybrid phenotypes is less well understood. In particular, it remains unclear whether a hybrid phenotype implies a mixture of the effects of several canonical lineages for each gene, or rather a bimodal behavior across genes. Th cell differentiation is a dynamic process in which the regulatory factors are modulated over time, but longitudinal studies of Th cell differentiation are sparse. Here, we present a dynamic transcriptome analysis following Th cell differentiation into Th1, Th2 and Th1/2 hybrid cells. We found that only a minority of ~20% of Th cell specific genes clearly shows mixed effects from both Th1 and Th2 cells on Th1/2 hybrid cells. While most genes follow either Th1 or Th2 cell gene expression, another fraction of ~20% of genes follows a Th1 and Th2 cell independent transcriptional program under control of the transcription factors STAT1 and STAT4. Overall, our results emphasize the key role of high-resolution longitudinal data for the characterization of cellular phenotypes.
2022-08-05 | GSE200250 | GEO