Chromatin Accessibility of LPS stimulated Activated B cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE208255 | GEO | 2023/06/20
REPOSITORIES: GEO
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Project description:We have generated a miR-17~92 fl/fl allele whose expression can be turned off conditionally by Cre recombinase in the miR-106a-363-/-;miR-106b-25-/- background. The mice were crossed to CD19-Cre mice to turn off the expression of miR-17~92 specifically in B cells and stimulated LPS/IL-4 for 13.5hr. Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 fl/fl;miR-106a-363;miR-106b~25 mice (TKO1, TKO2, TKO3) and WT (WT1, WTl2, WT3) by MACS depletion of cells positive for CD9, CD43, and CD93 (also known as AA4.1). The purified B cells were stimulated with LPS/IL-4 for 13.5hr in B cell media. The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).
2014-04-01 | E-GEOD-56378 | biostudies-arrayexpress
Project description:Murine B cells can be activated via the surface receptors TLR4 and CD40. For a global assessment of differences in gene expression between these two different modes of B cell activation a genome wide transcriptome analysis was performed. In order to dissect different gene expression profiles of B cells, activation was induced by LPS or LPS + anti-CD40 for 24h and 72h. Both activation states were compared to each other but also to naM-CM-/ve B cells. Gene expression profiles of naM-CM-/ve B cells, B cells activated with LPS and B cells activated with LPS + anti-CD40. Affymetrix MG 430 2.0 whole genome arrays were performed in quadruplicates for naM-CM-/ve B cells, B cells activated via TLR4 for 24 h and 72 h, and B cells activated via TLR4 + CD40 for 24 h and 72 h (20 arrays in total). To obtain genes significantly regulated upon stimulation with LPS, the expression profiles of naM-CM-/ve B cells, B cells activated with LPS for 24 h, and B cells activated with LPS for 72 h were compared to each other. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 M-BM-5g cRNA hybridized in quadruplicates for each of the five groups to the 20 GeneChip arrays: Group1 naM-CM-/ve B cells, Group2 LPS activated B cells 24h, Group3 LPS + anti-CD40 activated B cells 24h, Group4 LPS activated B cells 72h, and Group5 LPS + anti-CD40 activated B cells 72h. Access to PDF: http://dx.doi.org/10.1038/nature12979 All chips were imported into BioRetis (http://www.bioretis-analysis.de) and are open to the community now. If you want to obtain one or more lists of HPCDA significant genes you should click on a link of single chips (e.g. GSM879034) to get a description how to manage this.
2014-02-24 | E-GEOD-35998 | biostudies-arrayexpress
Project description:LPS activated murine splenic B cells (aB) were subjected to FAIRE-Seq, STARR-Seq, Hi-C, ChIP-seq, Nascent-RNA-seq and RNAseq to compile cis-regulome.
2019-12-23 | GSE121753 | GEO
Project description:Siglec-E is a murine CD33-related siglec that functions as an inhibitory receptor and is expressed mainly on neutrophils and macrophage populations. Recent studies have suggested that siglec-E is an important negative regulator of LPS-TLR4 signalling and one report (Wu et al 2016) claimed that siglec-E is required for TLR4 endocytosis following uptake of Escherichia coli by macrophages and dendritic cells (DCs). Our attempts to reproduce these observations using cells from wildtype (WT) and siglec E deficient mice were unsuccessful. We used a variety of assays to determine if siglec-E expressed by different macrophage populations can regulate TLR-4 signalling in response to LPS, but found no consistent differences in cytokine secretion in vitro and in vivo, comparing 3 different strains of siglec-E-deficient mice with matched WT controls. No evidence was found that the siglec-E deficiency was compensated by expression of siglecs-F and –G, the other murine inhibitory CD33-related siglecs. Quantitative proteomics was used as an unbiased approach and provided additional evidence that siglec-E does not suppress inflammatory TLR4 signaling. Interestingly, proteomics revealed a siglec E dependent alteration in macrophage phenotype that could be relevant to functional responses in host defence. In support of this, siglec-E-deficient mice exhibited enhanced growth of Salmonella enterica serovar Typhimurium in the liver following intravenous infection, but macrophages lacking siglec-E did not show altered uptake or killing of bacteria in vitro. Using various cell types including bone marrow derived DCs (BMDC), splenic DCs and macrophages from WT and siglec-E-deficient mice, we showed that siglec-E is not required for TLR4 endocytosis following E.coli uptake or LPS challenge. We failed to see expression of siglec-E by BMDC even after LPS-induced maturation, but confirmed previous studies that splenic DCs express low levels of siglec-E. Taken together, our findings do not support a major role of siglec-E in regulation of TLR4 signalling functions or TLR4 endocytosis in macrophages or DCs. Instead, they reveal that induction of siglec-E by LPS can modulate the phenotype of macrophages, the functional significance of which is currently unclear.
2018-02-09 | PXD008406 | Pride
Project description:To identify transcriptionally regulated genes in primary mouse macrophages stimulated with LPS with high sensitivity, we isolated nascent RNA following metabolic labelling with 4-thiouridine during the last 35 min before cell harvest, as recently described (Dolken et al. 2008 RNA 14:1959-72). Microarray analyses of nascent RNA identified substantially more probe sets as up-regulated after 45 min of LPS stimulation than parallel analyses of total cellular RNA. In contrast, 4.5 h after stimulation, up-regulated genes in total and nascent RNA largely overlapped. This approach therefore allowed a much more sensitive detection of early changes in transcription, and the respective genes are likely to be direct targets of LPS-regulated transcription factors. Keywords: Effect of LPS stimulation; comparison of changes in expression of total versus nascent RNA; timecourse
2010-04-25 | GSE20674 | GEO
Project description:Gene expression profiels in the human monocyte-derived dendritic cells (DCs) from 4 different donors (A, B, C, and D) were studied. Cells were left untreated (Group 4), activated with LPS alone (Group 1) or activated in the presence cmv IL-10 (Group 2) or human IL-10 (Group 3) for 12 hours before subjected to RNA extraction. Keywords: IL-10, LPS, dendritic cells
2007-02-22 | GSE7095 | GEO
Project description:Activation of the Mitogen activated protein kinase (MAPK) cascade following Toll-like receptor (TLR) stimulation enables innate immune cells to rapidly activate cytokine gene expression. A balanced response to signals of infectious danger requires that cellular activation is transient. Here, we identify the MAPK phosphatase Dual specificity phosphatase-1 (DUSP1) as an essential endogenous regulator of the inflammatory response to LPS. DUSP1-deficient (DUSP1-/-) bone marrow derived macrophages showed selectively prolonged activation of p38 MAPK and increased cytokine production. Intraperitoneal challenge of DUSP1-/- mice with LPS caused increased lethality and overshooting production of IL-6 and TNF?. Transcriptional profiling revealed that DUSP1 controls a significant fraction of LPS-induced genes, that includes IL-6 and IL-10 as well as the chemokines CCL3, CCL4 and CXCL2. In contrast, the expression of the important mediators of endotoxin lethality, IFN? and IL-12, was not significantly altered by the absence of DUSP1. These data together demonstrate a specific regulatory role of DUSP1 in controlling a subset of LPS-induced genes that determines the outcome of endotoxin shock. Keywords: in vivo analysis of splenic mRNA expression
2005-12-15 | GSE3565 | GEO
Project description:We have generated a miR-17-92 transgenic allele (termed miR-17-92 Tg) whose expression can be turned on conditionally by Cre recombinase (Xiao et al, Nature Immunology, 9:405-14, 2008). The mice were crossed to CD19-Cre mice to turn on the transgene expression specifically in B cells. Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 Tg/Tg mice (TG1, TG2, TG3) and miR-17~92 Tg/Tg mice (WT1, WT2, WT3) by MACS depletion of cells positive for CD5, CD43, and CD93 (also known as AA4.1). The purified B cells were stimulated with LPS/IL-4 for 13.5hr or 25.5hr. The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).
2014-04-01 | E-GEOD-56377 | biostudies-arrayexpress
Project description:Under microscope, MH-S cells show a heterogenous population. By clonal dilution, we generated single cell colonies and found that a set of clones that secreted higher the IL-4Ra regulating protein (“High IL-4Ra activity clones”) and set of colonies secreted lower amount (“Low IL-4Ra activity clones”). We performed microarrays to detail the global gene expression analysis comparing high IL-4Ra activity and low IL-4Ra activity MH-S clones stimulated with or without LPS. At this time point, roughly 50 genes annotated as “extracellular” were significantly upregulated more than two-fold in LPS stimulated clones compared to unstimulated ones. Of these, only seven genes showed higher expression in the high IL-4Ra activity clones compared to low IL-4Ra activity clones.
2020-03-02 | GSE134047 | GEO
Project description:To identify transcriptionally regulated genes in primary mouse macrophages stimulated with LPS with high sensitivity, we isolated nascent RNA following metabolic labelling with 4-thiouridine during the last 35 min before cell harvest, as recently described (Dolken et al. 2008 RNA 14:1959-72). Microarray analyses of nascent RNA identified substantially more probe sets as up-regulated after 45 min of LPS stimulation than parallel analyses of total cellular RNA. In contrast, 4.5 h after stimulation, up-regulated genes in total and nascent RNA largely overlapped. This approach therefore allowed a much more sensitive detection of early changes in transcription, and the respective genes are likely to be direct targets of LPS-regulated transcription factors. Keywords: Effect of LPS stimulation; comparison of changes in expression of total versus nascent RNA; timecourse Two completely independent experiments were performed. Macrophages were stimulated with 100 ng/ml LPS for 45 or 270 minutes. Thiouridine pulsing was done in last 35 minutes before harvest. Total RNA was isolated. Nascent RNA was subsequently purified.
2010-05-07 | E-GEOD-20674 | biostudies-arrayexpress