RNA-seq of Th1 and Th2 differentiated T helper cells re-stimulated with pma/ionomycin after 7 days of differentiation.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB41969 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4982120.fastq.gz | Fastqsanger.gz | |||
| ERR4982121.fastq.gz | Fastqsanger.gz | |||
| ERR4982122.fastq.gz | Fastqsanger.gz | |||
| ERR4982123.fastq.gz | Fastqsanger.gz | |||
| ERR4982124.fastq.gz | Fastqsanger.gz |
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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.
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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: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.
2022-05-06 | E-MTAB-9819 | 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:Background: Our purpose was to obtain non-existing genome-wide expression data for the rabbit species on the responses of peripheral blood mononuclear cells (PBMCs) after in vitro stimulation by lipopolysaccharide (LPS) or phorbol myristate acetate (PMA) and ionomycin. This transcriptomic study was carried out using microarrays enriched with immunity-related genes, and annotated with the most recent data available for the rabbit genome. Results: The LPS affected 15 to 20 less genes than PMA/Ionomycin after 4 hours (T4) or 24 hours (T24), of in vitro stimulation, by comparison with mock-stimulated PBMCs. LPS induced an inflammatory response as shown by a significant up-regulation of IL12A and CXCL11 at T4, followed by an increased transcription of IL6, IL1B, IL1A, IL36, IL37, TNF, CCL4 and SAA1 at T24. Surprisingly, we could not find an up-regulation of IL8 either at T4 or at T24. PMA/ionomycin induced a very early expression of Th1, Th2, iTreg, and Th17 responses by PBMCs at T4. The Th1 response was increased at T24 as shown by the increase of the transcription of IFNG and by contrast to other cytokines that significantly decreased from T4 to 24 (IL2, IL4, IL10, IL13, IL17A, CD69). The granulocyte-macrophage colony-stimulating factor (CSF2) was by far the most over-expressed gene at both T4 and T24 by comparison to mock-stimulated cells, confirming a major impact of PMA/ionomycin on cell growth and proliferation. A significant down-regulation of IL16 was observed at T4 and T24, in agreement with a role of IL16 in in PBMC apoptosis. Conclusion: We report new data on the responses of PBMCs to LPS and PMA/ionomycin for the rabbit species, thus enlarging the set of mammalian species for which such reports exist. The availability of the rabbit genome assembly together with highly performing genomic tools should pave the way for more intense genomic studies for this species known to be a very relevant animal model in immunology and physiology.
2014-07-10 | GSE59263 | GEO
Project description:Background: Our purpose was to obtain non-existing genome-wide expression data for the rabbit species on the responses of peripheral blood mononuclear cells (PBMCs) after in vitro stimulation by lipopolysaccharide (LPS) or phorbol myristate acetate (PMA) and ionomycin. This transcriptomic study was carried out using microarrays enriched with immunity-related genes, and annotated with the most recent data available for the rabbit genome. Results: The LPS affected 15 to 20 less genes than PMA/Ionomycin after 4 hours (T4) or 24 hours (T24), of in vitro stimulation, by comparison with mock-stimulated PBMCs. LPS induced an inflammatory response as shown by a significant up-regulation of IL12A and CXCL11 at T4, followed by an increased transcription of IL6, IL1B, IL1A, IL36, IL37, TNF, CCL4 and SAA1 at T24. Surprisingly, we could not find an up-regulation of IL8 either at T4 or at T24. PMA/ionomycin induced a very early expression of Th1, Th2, iTreg, and Th17 responses by PBMCs at T4. The Th1 response was increased at T24 as shown by the increase of the transcription of IFNG and by contrast to other cytokines that significantly decreased from T4 to 24 (IL2, IL4, IL10, IL13, IL17A, CD69). The granulocyte-macrophage colony-stimulating factor (CSF2) was by far the most over-expressed gene at both T4 and T24 by comparison to mock-stimulated cells, confirming a major impact of PMA/ionomycin on cell growth and proliferation. A significant down-regulation of IL16 was observed at T4 and T24, in agreement with a role of IL16 in in PBMC apoptosis. Conclusion: We report new data on the responses of PBMCs to LPS and PMA/ionomycin for the rabbit species, thus enlarging the set of mammalian species for which such reports exist. The availability of the rabbit genome assembly together with highly performing genomic tools should pave the way for more intense genomic studies for this species known to be a very relevant animal model in immunology and physiology. To characterize gene expression changes in peripheral blood mononuclear cells (PBMCs), we collected blood from 4 adult rabbits. PBMCs were isolated and stimulated with LPS or a mixture of PMA/Ionomycin, versus a control group (C). Cells were harvested either 4h or 24h after activation.
2014-07-10 | E-GEOD-59263 | biostudies-arrayexpress
Project description:To investigate gene regulation in response to T cell activation. We then performed gene expression profiling analysis using data obtained from RNA-seq of cell lines stimulated by PMA and Ionomycin.
2022-12-28 | GSE221851 | GEO
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
Project description:Background: During the past 25 years, selection of production traits highly increased pig production but diseases have emerged that may cause economic loss of extreme importance. Designing sustainable animal production that better balances productivity with resistance to disease is a major concern and challenge for the next decade. In order to address questions related to immunity and resistance to disease, it is necessary to increase knowledge on the pig immune system and to produce efficient tools dedicated to this species. In this context we produced a generic array enriched in immunity genes and validated its relevance by studying innate immune response of pigs by stimulating porcine mononuclear cells with lipopolysaccharide (LPS) or a mixture or phorboml myristate acetae (PMA) and ionomycin for 24 hours. Results: A long oligonucleotide-based chip was produced by combining a generic set of 13K probes targeting 8541 genes to a newly designed SLA-RI set that targets all genes and pseudogenes of the pig major histocompatibility complex region (SLA complex) in both orientations (906 probes) and immunity genes outside the SLA complex (2957 porbes). The porcine chip was referred to as SLA-RI/NRSP8-13K. Transcripotme analysis of PBMCs stimulated by LPS or PMA/ionomycin was carried out. Ten times more genes were up regulated after PMA/ionomycin stimulation by comparison to LPS stimulation. The LPS response was more related to the catalog Diseases and Disorders and the PMA/ionomycin response to the catalog Molecular and Cellular Function. LPS stimulation induced a general inflammation response with over-expression of SAA1, pro-inflammatory chemokines IL8, CCL2, CXCL5, CXCL3, CXCL2 and CCL8 as well as genes related to oxidative processes (SOD2) and calcium pathways (S100A9 and S100A12). PMA/ionomycin stimulation induced a stronger up-regulation of T cell activation than B cell activation with dominance toward a Th1 response, including IL2, CD69 and TNFRSF9 genes. In addition, a very intense repression of THBS1 was observed, suggesting a predominant role of this matricellular glycoprotein during T/B cell stimulation by tumor inducers. Repression of MHC class I genes was observed after PMA/ionomycin stimulation despite an up-regulation of the gene cascade involved in peptide processing and repression of MHC class II genes was observed after both stimulations. A significant reduction of antigen presentation to T cells was shared by the two types of responses that is likely to be due to separate mechanisms that need further elucidation. In addition, our results provided preliminary data suggesting a role of antisense transcripts mapping to the SLA complex during immune response. Conclusion: The SLA-RI/NRSP8-13K was highly relevant to. On the one hand the SLA-RI/NRSP8-13K was shown to be relevant and accurate to decipher two distinct innate immune responses by PBMCs indicating that this chip will constitute a valuable tool to further study immunity and resistance to disease in pig. On the other hand, the transcriptom analysis revealed specific and common features of the innate immune response according to stimulation that increase knowledge on pig immunity. Keywords: immune response activation in pig PBMCs
2010-01-31 | GSE17320 | GEO
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