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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression by cyotosolic DNA stimulation

ABSTRACT: STING molecule has been reported to be important adaptor molecule for cytosolic DNA sensing. We investigated gene expression by cytosolic DNA stimulation using bone marrow derived dendritic cells. We comparared gene expression profile between WT and STING knock out BMDCs after cytosolic DNA stimulation. We generated BMDCs by culturing in the presence of GM-CSF. BMDCs were stimulated by purified tumor-cell derived DNA using lipofectamine. After 7 hrs incubation, total RNA was isolated using Rneasy kit (Qiagen) and microarray was performed at genomic core facility in university of Chicago

ORGANISM(S): Mus musculus

SUBMITTER: Seng-Ryong Woo

PROVIDER: E-GEOD-61835 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression by cyotosolic DNA stimulation

Project description:STING molecule has been reported to be important adaptor molecule for cytosolic DNA sensing. We investigated gene expression by cytosolic DNA stimulation using bone marrow derived dendritic cells. We comparared gene expression profile between WT and STING knock out BMDCs after cytosolic DNA stimulation.

2014-09-30 | GSE61835 | GEO

Gene expression profiling of human telomerase fibroblasts stimulated with dsDNA90

Project description:Gene expression analysis of dsDNA90 stimulated human telomerase fibroblasts (hTERT-BJ1) after STING siRNA treatment. Genes whose expression that are affected by cytosolic DNA in a STING dependent manner will be identified and signaling pathways regulated by STING will be elucidated. hTERT-BJ1 cells were transfected with non-specific or STING siRNA for 72 hours followed by dsDNA90 stimulation for 3 hours. Total RNA was extracted for array analysis.

2013-01-15 | E-GEOD-43480 | biostudies-arrayexpress

Identification of Nrf2 regulated genes by RNA sequencing

Project description:The transcription factor Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is activated by the metabolite itaconate during metabolic reprogramming. Activated Nrf2 then dampens the release of pro-inflammatory cytokines and type I IFNs in response to toll-like receptor stimulation. If and how Nrf2 affects cytosolic antiviral sensing and whether this occurs during metabolic reprogramming is currently not known. Here, we show that Nrf2 is a negative regulator of the adaptor molecule STimulator of INterferon Genes (STING), which signals downstream of the cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS). The regulation of STING by Nrf2 was inducible by the metabolite itaconate, specific to human cells, and sufficient to decrease the responsiveness to STING agonists and to increase the susceptibility to infection with DNA viruses. Mechanistically, Nrf2 regulated STING expression post-transcriptionally by increasing STING mRNA stability. Lastly, treatment with itaconate or with the chemical Nrf2 inducer sulforaphane repressed STING expression and the release of type I IFNs in cells from patients with the STING dependent interferonopathy SAVI. With this report we identify Nrf2 as an important regulator of cGAS-STING signaling pathway and link metabolic reprogramming to control of cytosolic DNA sensing.

2018-05-01 | GSE113519 | GEO

Transcription profiling of mouse dendritic cells reveals stimulatory effect of Echinacea purpurea extract on trafficking activity

Project description:To seek scientific evidence supporting therapeutic use of Echinacea, the transcriptomic effects of Echinacea purpurea extract on mouse bone marrow-derived dendritic cells (BMDCs) were analyzed using primary cultures. Affymetrix DNA microarray and bioinformatics analyses of genes differentially expressed in DCs treated with [BF/S+L/Ep] for 4 or 12 h revealed that the majority of responsive genes were related to cell adhesion or motility (Cdh10, Itga6, Cdh1, Gja1 and Mmp8), or were chemokines (Cxcl2, Cxcl7) or signaling molecules (Nrxn1, Pkce and Acss1). Experiment Overall Design: BMDCs from mice were treated with [BF/S+L/Ep] or DMSO for 4 h or 12 h in duplicates.

2009-12-14 | E-GEOD-19369 | biostudies-arrayexpress

Expression data from BMDCs treated with BI2536 or vehicle control and stimulated with LPS or poly(I:C)

Project description:We used microarrays to detail the global programme of gene expression underlying Polo-like kinase inhibition with BI 2536 compound in mouse bone marrow-derived dendritic cells (BMDCs) stimulated with Toll-like receptor agonists LPS and poly(I:C). CD11c+ BMDCs were treated for 1 hour with BI 2536 (1µM) or vehicle control (DMSO) prior to stimulation with LPS or poly(I:C) for 4 h. Total RNA was extracted and prepared for hybridization on Affymetrix microarrays.

2011-04-12 | E-GEOD-28520 | biostudies-arrayexpress

Ad-MyD88 infected bmDCs: Control vs. Ad-MyD88 infected

Project description:Transcriptional profiling of Bone-Marrow derived mouse Dendritic Cells (bmDCs) infected with Ad-MyD88 vs. Ad-GFP or mock infected Three-condition experiment, Ad-MyD88 vs. Ad-GFP vs. Mock infected cells. Biological replicates: 3 Ad-MyD88, 3 Ad-GFP, 3 mock, independently grown and harvested. One replicate per array.

2010-10-08 | E-GEOD-19006 | biostudies-arrayexpress

Transcription profiling of mouse bone marrow-derived dendritic cells stimilated with LPS in the presence or absence of cAMP

Project description:genes regualted by LPS or LPS+cAMP stimulation in BMDCs; We used microarrays to identify genes that up-regulated by LPS+cAMP compared with just LPS. Experiment Overall Design: BMDCs were stimilated with LPS (10 ng/ml) in the presence or absence of cAMP (100 microM) for 3h. Specifically up-regualted gene by cMP was identified.

2009-07-05 | E-GEOD-16761 | biostudies-arrayexpress

Gene expression profiling in wild-type, Irf5-KO, Lyn-KO and Lyn/Irf5-DKO BMDCs unstimulated or stimulated with CpG-B ODN

Project description:To characterize the relationship between IRF5 and Lyn in innate immune responses at a genome-wide scale, we performed gene expression microarray analysis for wild-type (WT), Irf5-KO, Lyn-KO and Lyn/Irf5-DKO bone marrow-derived dendritic cells (BMDCs) with or without 6 h-stimulation with 150 nM CpG-B ODN. We extracted the transcripts that were upregulated by CpG-B ODN in WT BMDCs, further upregulated in Lyn-KO BMDCs and then downregulated in Lyn/Irf5-DKO BMDCs (fold change â?¥ 2, false discovery rate < 0.05). When these 79 transcripts were sorted by their expression levels in Lyn-KO BMDCs, most of the top 20 genes (13 out of 20) were those encoding type I interferons (IFNs), indicating that Lyn particularly suppresses IRF5 induction of type I IFNs. BMDCs from WT, Irf5-KO, Lyn-KO and Lyn/Irf5-DKO mice in a C57BL/6 background were unstimulated or stimulated with CpG-B ODN. Biological triplicate for each genotype were analyzed (24 samples in total).

2016-07-25 | E-GEOD-63014 | biostudies-arrayexpress

Differential gene regulation downstream of murine Tmem173 variants

Project description:We report positional cloning and characterization of a novel Sting allele that fails to activate IFN production in the wild-derived mice of MOLF/Ei strain in response to HSV (Herpes Simplex Virus) and Listeria monocytogenes both in vitro and in vivo. We show that previously uncharacterized mutations in the N-terminal of STING are responsible for low levels of IFN due to failure of MOLF STING to respond to cytosolic STING agonists such as 2â3âcGAMP, 5,6-Dimethylxanthenone-4-acetic acid (DMXAA) or poly(deoxyadenylic-deoxythymidylic) acid (dAdT). Using Next-Generation Sequencing (NGS) for the analysis of DNA-responses in congenic C57BL6.StingMOLF/MOLF (MOLF STING) mouse macrophages, we show that these mutations in MOLF/Ei discriminate in responses between different STING agonists. Macrophages from C57BL6.StingB6/B6Â¬ (B6 STING), or B6 STING expressing littermates were stimulated as a positive control for STING activation, and STING -/- (STING KO) macrophages served as a negative control. To examine differential gene regulation downstream of murine Tmem173 (STING) allelic variants. We stimulated macrophages from B6 mice congenic for MOLF STING; macrophages from B6 STING expressing littermates were stimulated as a positive control for STING activation, and STING -/- (STING KO) macrophages served as a negative control. One replicate of RNA-seq reads after each stimulation provided. Conditions are peritoneal macrophages from B6 congenic mice expressing: B6 STING, MOLF STING, or STING KO stimulated with 2â3âcGAMP, 5,6-Dimethylxanthenone-4-acetic acid (DMXAA), poly(deoxyadenylic-deoxythymidylic) acid (dAdT), or no treatment. This constitutes a total of 12 reads analyzed in this data set.

2016-07-05 | E-GEOD-68140 | biostudies-arrayexpress

CT26 sorted in vivo tumor cells with Trex1 KO

Project description:The DNA exonuclease TREX1 degrades endogenous cytosolic DNA. Cytosolic DNA triggers the cGAS/STING pathway which increases type I interferon. To investigate the physiological significance of TREX1 loss on in vivo tumor growth, we implanted control and TREX1-deficient CT26 tumor cells into immunocompetent BALB/c hosts.Tumor cells were collected 7 days after tumors reached around 200mm3.

2024-03-12 | E-MTAB-13816 | biostudies-arrayexpress

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