Expression data from Daudi cells stimulated with anti-CD40 and/or IL-4 for 6 hr with or without AICAR-pretreatment
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE4812 | GEO | 2006/07/31
SECONDARY ACCESSION(S): PRJNA95615
REPOSITORIES: GEO
Similar Datasets
Project description:We used microarrays to detail the transcriptome response to CD40-ligation and IL-4 stimulation in Daudi cells. Keywords: gene expression array-based, response to anti-CD40 and/or IL-4
2006-07-31 | GSE4846 | GEO
Project description:Purpose: To gain insight into both similarities and differences in the gene expression programs induced by IL-21R, BCR and CD40 signals, we performed RNA-seq on both GCBC and NBC that had been stimulated for either 2h or 4h with IL-21, CD40 ligation, BCR ligation, or combinations of these. Methods : Purified GCBC from d14 NP-CGG immunized MEG mice and NBC from naïve MEG mice were warmed at 37C for 30 minutes and then stimulated with 10ng/mL IL-21, 20μg/ml ⍺-IgM or 2.5μg/mL ⍺-CD40 (prepared as tetramer) alone or combined IL21/⍺-CD40 or ⍺-IgM/⍺-CD40 for 2 and 4 hours. After stimulation, cells were processed for RNA isolation using QIAshredder columns (Qiagen) and the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. Samples were sequenced using Illumina NextSeq 500 with 75 bp paired-end reads and aligned to the mm10 genome using the STAR aligner (Dobin et al., 2013). Gene-level counts were determined using featureCounts (Liao et al., 2014), and raw counts were quantile normalized to each other for differential expression using the voom method (Law et al., 2014) in the Limma R package (Ritchie et al., 2015). For normalization of the datasets, the Quantile method was used. Results: Like BCR and CD40 signals, IL-21R plus CD40 signals also synergize to induce c-Myc in GCBC. However, IL-21R plus CD40 stimulation differentially affects GCBC fate compared to BCR plus CD40 ligation—engaging unique molecular mechanisms
2023-02-16 | GSE197662 | GEO
Project description:The interaction between the transmembrane glycoprotein surface receptor CD40 expressed by skin keratinocytes (KCs) and its T cell-expressed ligand CD154 was suggested to exacerbate inflammatory skin diseases. However, the full spectrum of CD40-mediated effects by KCs underlying this observation is unknown. Therefore, changes in gene expression after CD40 ligation of KCs were studied by microarrays. CD40-mediated activation for 2 hours stimulated the expression of a coordinated network of immune-involved genes strongly interconnected by IL8 and TNF, while after 24 hours anti-proliferative and anti-apoptotic genes were upregulated. CD40 ligation stimulated the production of chemokines that attracted lymphocytes and myeloid cells from peripheral blood mononuclear cells (PBMCs). Thus, CD40-mediated activation of KCs resulted in a highly coordinated response of genes required for the local development and sustainment of adaptive immune responses. The importance of this process was confirmed by a study on the effects of human papilloma virus (HPV) infection to the KCâs response to CD40 ligation. HPV infection clearly attenuated the magnitude of the response to CD40 ligation and consequently the KCâs capacity to attract PBMCs. The fact that HPV attenuates CD40 signalling in KCs indicates the importance of the CD40-CD154 immune pathway in boosting cellular immunity within epithelia. Total RNA from eight 72 hours 50 IU/ml IFNgamma pre-stimulated primary undifferentiated keratinocyte cultures, four uninfected and four HPV-positive, that were either left unstimulated, or stimulated for 2 hours with IFNgamma and Control- or CD40L-expressing L-cells (mouse fibroblasts), or stimulated for 24 hours with IFNgamma and Control- or CD40L-expressing L-cells. The stimulated samples were generated in duplo. 72 samples were generated in total.
2015-10-26 | E-GEOD-54181 | biostudies-arrayexpress
Project description:The interaction between the transmembrane glycoprotein surface receptor CD40 expressed by skin keratinocytes (KCs) and its T cell-expressed ligand CD154 was suggested to exacerbate inflammatory skin diseases. However, the full spectrum of CD40-mediated effects by KCs underlying this observation is unknown. Therefore, changes in gene expression after CD40 ligation of KCs were studied by microarrays. CD40-mediated activation for 2 hours stimulated the expression of a coordinated network of immune-involved genes strongly interconnected by IL8 and TNF, while after 24 hours anti-proliferative and anti-apoptotic genes were upregulated. CD40 ligation stimulated the production of chemokines that attracted lymphocytes and myeloid cells from peripheral blood mononuclear cells (PBMCs). Thus, CD40-mediated activation of KCs resulted in a highly coordinated response of genes required for the local development and sustainment of adaptive immune responses. The importance of this process was confirmed by a study on the effects of human papilloma virus (HPV) infection to the KC’s response to CD40 ligation. HPV infection clearly attenuated the magnitude of the response to CD40 ligation and consequently the KC’s capacity to attract PBMCs. The fact that HPV attenuates CD40 signalling in KCs indicates the importance of the CD40-CD154 immune pathway in boosting cellular immunity within epithelia.
2015-10-26 | GSE54181 | GEO
Project description:Ribonucleoside AICAr, a precursor in purine synthesis and a known activator of AMPK, was shown to induce monocytic differentiation in AML cell lines by inducing pyrimidine depletion followed by activation of ATR/Chk1 pathway and cell cycle arrest. Here we report transcriptional changes induced by AICAr in the primary AML sample (FAB-M2, FLT3 negative, NPM1 negative) in which AICAr induced differentiation and accumulation of macrophage cells in vitro. RNA-seq transcriptome analysis of primary AML cells isolated from the bone marrow of a patient with de novo FAB-M2 AML. Mononuclear cells were isolated from the bone marrow sample by density gradient separation and grown in RPMI supplemented with 10% FBS, 2 mM L-glutamine, 50 U/ml penicillin, 50 μg/ml streptomycin and 50 ng/ml IL-3, IL-6, SCF and FLT3L. Cells were treated with AICAr (0.4 mM) for 24 h. Experiment was performed in biological triplicates and total RNA was isolated for transcriptome analysis using Illumina high throughput sequencing.
2020-11-01 | E-MTAB-9209 | biostudies-arrayexpress
Project description:AICAR monophosphate (5-Aminoimidazole-4-carboxamide ribonucleotide) is a metabolic intermediate of the de novo purine synthesis pathway presenting highly promising metabolic and antiproliferative properties. Yeast mutants accumulating AICAR are auxotroph for histidine. A screening for suppressors of this phenotype identified recessive and dominant mutants that result in lowering intracellular AICAR concentration. The recessive mutants affect adenosine kinase which is shown here to catalyze the phosphorylation of AICAR riboside in yeast. The dominant mutants strongly enhance the capacity of the alkaline phosphatase Pho13p to dephosphorylate succinyl-AICAR monophosphate into the non-toxic riboside form. By combining these mutants to transcriptomic and metabolomic analyses, we establish that in yeast both toxic and physiological responses to AICAR are linked to the concentration of the monophosphate form, while the nucleoside moiety has no effect even at high concentration. Finally, we establish that (S)AICAR concentration varies under physiological conditions, thus modulating transcriptional regulation of purine pathway genes. This SuperSeries is composed of the SubSeries listed below.
2011-07-11 | GSE29324 | GEO
Project description:Purpose:Flow cytometric analysis showed that after 48h of culture with T cell- and Ag-derived stimuli, GCBC alter their TF expression and begin to differentiate. However, only a subset of cells undergoes this process, for reasons that are unclear. To better define the nature of this heterogeneity, and to further define the differences between IL-21R/CD40 vs BCR/CD40 signals, we performed single cell RNA-seq (scRNA-seq) of 48h GCBC cultures with either of these two stimuli or with the combination of IL-21R/CD40 and BCR stimulation. Methods: we performed scRNA-seq using 10X Genomics Chromium system . Results: Single cell analysis demonstrated surprisingly little overlap between the clusters derived from IL-21/⍺-CD40 stimulation and those derived from BCR/⍺-CD40 ligation, thus establishing at molecular and cellular detail how distinct these two types of selection signals are for GCBC
2023-02-16 | GSE197661 | GEO
Project description:The purpose of the research is to delineate the mechanism behind AICAR-induced cytotoxicity by understanding the genetic pathways that are affected with AICAR treatment.
2023-02-21 | GSE198777 | GEO
Project description:To identify genes transcriptionally regulated by AICAR under cellular stress, We treated NALM6 cells for 45 min with vehicle (DMSO) or AICAR (15 mM), and examined their RNA profile using RNA-Seq. The immediate early genes (IEGs) were identified as a subset of genes downregulated by AICAR.
2021-07-22 | GSE152917 | GEO
Project description:Study of the effect of SP140 deletion on the distribution of H3K27me3 in two independent Burkitt''s Lymphoma cell lines (DAUDI and Ramos).
2024-11-21 | GSE229801 | GEO