Ontology highlight
ABSTRACT:
PROVIDER: PRJNA453806 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7083010.fastq.gz | Fastqsanger.gz | |||
| SRR7083020.fastq.gz | Fastqsanger.gz | |||
| SRR7083030.fastq.gz | Fastqsanger.gz | |||
| SRR7083040.fastq.gz | Fastqsanger.gz | |||
| SRR7083050.fastq.gz | Fastqsanger.gz |
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Project description:NFKB is a family of transcription factors (TF), which are master regulators of the innate immune system. It is activated downstream of pathogen recognition receptors after ligand binding and regulates the expression of antimicrobials, cytokines and chemokines, thus helping to fight infections as well as recruiting the adaptive immune system. Although NFKB responds to a wide variety of signals, the processes in which stimulus-specificity is attained are still unclear. Here, we characterized the response of one of the NFKB members, RELA, to five stimuli mimicking infection in nasopharyngeal epithelial cells. When comparing RELA genome-wide binding sites , we detected most of them to be overlapping among the different stimulations. Yet, we distinguished a minority of stimulus-specific RELA binding sites. Interestingly, some of these seemed to have a biological effect as they correlated with corresponding gene expression. Specifically, the response to Poly I:C mimicking viral dsRNA gave a distinct RELA profile binding the vicinity of antiviral genes. This group of binding sites was also enriched in Interferon Regulatory Factor motifs indicating that the interaction with more specialized TFs could contribute to stimulus-specific RELA activity. Furthermore, motif analysis revealed differences in the sequence of the NFKB motifs between certain stimulus-specific sets of peaks suggesting preferences for particular NFKB dimers in response to defined signals.
2018-01-30 | GSE91018 | GEO
Project description:NFKB is a family of transcription factors (TF), which are master regulators of the innate immune system. It is activated downstream of pathogen recognition receptors after ligand binding and regulates the expression of antimicrobials, cytokines and chemokines, thus helping to fight infections as well as recruiting the adaptive immune system. Although NFKB responds to a wide variety of signals, the processes in which stimulus-specificity is attained are still unclear. We characterized the response of one of the NFKB members, RELA, to five stimuli mimicking infection in nasopharyngeal epithelial cells. We wanted to investigate gene expression in response to these stimuli as well, in order to relate RELA binding to differences to expression regulation. Although most RELA binding sites where common among stimulation, we distinguished a minority of stimulus-specific RELA binding sites. Interestingly, some of these seemed to have a biological effect as they correlated with corresponding gene expression. Especially, the response to Poly I:C mimicking viral dsRNA gave a distinct RELA profile binding the vicinity of antiviral genes. Some of which were overexpressed under Poly I:C stimulation specifically.
2018-01-30 | GSE91019 | GEO
Project description:Analyses of the whole genome mRNA gene expression profiling performed on Lpar6+/+ and Lpar6-/- mouse embryonic fibroblasts (MEFs). The Lpar6-/- MEFs showed higher proliferation rate. The LPAR6 knock-down cells displayed NFkB and STAT3 pathway actvation and downregulation of AHR and TRIM24 pathway.
2024-07-17 | GSE49157 | GEO
Project description:Epigenetic modifications play crucial roles on establishment of tissue-specific transcription profiles and cellular characteristics. Direct conversions of fibroblasts into differentiated tissue cells by over-expression of critical transcription factors have been reported, but the epigenetic mechanisms underlying these conversions are still not fully understood. In addition, conversion of somatic cells into germ cells has not yet been achieved. To understand epigenetic mechanisms that underlie germ cell characteristics, we attempted to use defined epigenetic factors to directly convert mouse embryonic fibroblasts (MEFs) into germ cells. Here, we successfully induced germ cell-specific genes by inhibiting repressive epigenetic modifications via RNAi or small-molecule compounds. Under these conditions, some tissue-specific genes and stimulus-inducible genes were also induced. Meanwhile, the treatments did not result in genome-wide transcriptional activation. These results suggested that a permissive epigenetic environment resulted in selective de-repression of stimulus- and differentiation-inducible genes including germ cell-specific genes in MEFs.
2016-09-09 | GSE86005 | GEO
Project description:RNAseq data from hMPDMs (HoxB4 myeloid progenitor derived macrophages), BMDMs (bone-marrow derived macrophages), and Raw264.7 cell line in unstimulated condition and 3 hours post LPS stimulation (lipopolysaccharide). Gene expression demonstrates similarities between hMPDMs and BMDMs supporting use of hMPDMs in this study of NFkB stimulus response signaling dynamics, whereas Raw264.7 cells are more distinct from BMDMs in terms of expression LPS-inducible genes.
2024-06-03 | GSE246566 | GEO
Project description:We here identified that the trimeric spike protein of SARS-CoV-2 could bind to TLR4 directly and robustly activate downstream signaling in monocytes and neutrophils. Moreover, specific TLR4 or NFKB inhibitor, or knockout of MyD88 could significantly block IL-1B induction by spike protein. We thus reveal that spike protein of SARS-CoV-2 functions as a potent stimulus causing TLR4 activation and sepsis related abnormal responses.
2021-02-25 | GSE167480 | GEO
Project description:According to current models, transcription factors (TFs) activated by extracellular stimuli operate in the context of a pre-established enhancer repertoire induced and maintained by lineage-specific TFs. Here, we uncovered the existence of latent enhancers, defined as regions of the genome that in terminally differentiated cells are poorly accessible and lack the histone marks characteristic of enhancers, but readily acquire these features in response to extracellular cues. Stimulation of resting macrophages caused simultaneous binding of stimulus-activated TFs and lineage-determining TFs to these regions, enabling deposition of enhancer-specific features. Once unveiled, these enhancers did not return to a latent state even when stimulation ceased; instead, they persisted and mediated a faster and stronger response upon restimulation. We suggest that stimulus-specific expansion of the available cis-regulatory repertoire provides an epigenomic memory of the exposure to environmental agents. Formaldehyde-Assisted Isolation Of Regulatory Elements (FAIRE) followed by multiparallel sequencing was performed in untreated murine bone marrow-derived macrophages.
2013-01-17 | E-GEOD-41677 | biostudies-arrayexpress
Project description:Reactive oxygen species (ROS) induced by ultraviolet B (UVB) cause DNA damage such as 8-oxoguanine (8-oxoG) in mouse skin, with long-term exposure leading skin tumor development. We previously reported that Ogg1 knockout mice, with defective repair enzyme for 8-oxoG oxidatively damaged DNA, showed greater up-regulation of inflammatory response genes and Versican, which encodes a large extracellular matrix proteoglycan, than their wild-type counterparts. Here, we focused on inflammatory response genes associated with Versican up-regulation after UVB exposure, using Ogg1 knockout mouse embryonic fibroblasts (MEFs). Gene profiling among inflammatory response-associated genes in MEFs treated with UVB showed that Cxcl1, a CXC chemokine, was most significantly up-regulated in Ogg1(-/-) MEFs, concomitant with the up-regulation of Versican. We found that Versican targeted siRNA directly regulated Cxcl1, and vice versa, in which the system of up-regulation for these two key genes were controlled by PI3kinase-NFkB activation signaling rather than conventional UV-induced p38 mitogen-activated protein kinase. Furthermore, for the initial process of differentiating inflammatory response between Ogg1(-/-) and Ogg1(+/+), we found that down-regulation of p53 along with anti-apoptotic signal was a key event in Ogg1(-/-).The results of the present study suggest suppression of skin tumor development involving UVB/ROS-induced 8-oxoG formation by targeting genes and signaling pathways.
2016-04-25 | GSE80362 | GEO
Project description:Developmental signals are known to modulate inflammation. How ever, the mechanistic insight that links developmental and inflammatory signaling remains elusive. In the current study, we identifya critical role of NF-kB system in mediating stimulus specific crosstalk that allows developmental LTbR signals to sustain inflammatory TLR4 induced RelA/NF-kB response and gene expression. LTbR activated non-canonical signaling targets canonical TLR4 induced, nfkb2 encoded p100 not only to deplete inhibitory IkBd/(p100)2, but also to supplement RelA:p52/NF-kB dimers. Robust crosstalk in the gut epithelial cells are important, as crosstalk-defective nfkb2-/- mice succumbed to gut infection by Citrobacter rodentium due to hypo-inflammatory responses. Finally, we present evidence for a crosstalk motif that integrates tissue microenvironment derived developmental cues to ameliorate the pathogen response. Total RNA from WT early passage MEFs stimulated with ligands LPS, LTbR and LPS+LTbR for 24hrs were analyzed for global gene expression levels
2015-05-01 | E-GEOD-62301 | biostudies-arrayexpress