Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1036700 | ENA |
REPOSITORIES: ENA
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Project description:Gene Expression changes in BMDCs stimulated with H. pylori vs. E. coli. The hypothesis tested was that the gene expression profile in BMDCs stimulated with H. pylori lysate will be less inflammatory than BMDCs stimulated with E. coli. BMDCs were generated from bone marrow of wild type female C57BL/6 mice using 100ng/mL Flt3L. DCs were harvested at day 8 and stimulated with either media alone, H. pylori antigen lysate or E. coli lysate. At 24 hours, the cells were harvested and RNA was isolated for microarray analysis.
2013-06-14 | E-GEOD-44954 | biostudies-arrayexpress
Project description:Purpose: The purpose of this study is to identify the genome-wide binding sites for IRF4 interaction partners PU.1, BATF, and JunB in dendritic cells. These ChIP-seq data were integrated with gene expression analysis in IRF4-sufficient and -deficient BMDCs in order to assemble an IRF4 gene regulatory network. Hematopoietic bone marrow progenitors from C57BL/6 mice were differentiated with GM-CSF and IL-4 for 5 days. On day 6, BMDCs were stimulated for 6 hours with 100ng/ml LPS. Fixed chromatin was immunoprecipitated with anti-PU.1, BATF, and JunB antibodies and subjected to high-throughput sequencing. The sequencing data for the input DNA was previously submitted as GSM999807.
2013-12-22 | E-GEOD-52772 | biostudies-arrayexpress
Project description:Introduction: DCs sense and respond to a variety of pathogen-dependent and independent features. We found that DCs can directly sense the presence of immunological memory in the form of effector memory T cells. This activation by effector memory T cells led to a robust inflammatory signature in interacting DCs. Method: Bone marrow derived DCs (BMDCs) were differentiated in the presence of GMCSF for 7 days. WT naïve T cells were polarized to Th0 (platebound anti-CD3 and anti-CD28 and soluble IL-2) for 5 days, followed by 2 days of rest in low IL-2 containing media to mimic generation of effector memory T cells. CD11c+ BMDCs were sorted via AutoMacs and activated with LPS (100ng/mL) or effector memory T cells (ratio of 1:4) in the presence or absence of soluble anti-CD3 (200ng/mL) for 3 hours. Cells were blocked with FC block and stained with flourophores to distinguish DCs from T cells. DCs were FACS sorted and lysed in Trizol. Conclusion: BMDCs activated with LPS or effector memory T cells had a distict transcriptional response. When activated with effector memory T cells, BMDCs upregulated genes associated with TNFRSF signaling. BMDCs activated with LPS or effector memory T cells also shared certain transcriptional features of upregulated cytokine and chemokine expression.
2021-11-30 | GSE184607 | GEO
Project description:The transcriptional coactivator ANGUSTIFOLIA 3 (AN3) stimulates cell proliferation during Arabidopsis leaf development, but the molecular mechanism is largely unknown. We show here that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR 2 (CRF2), CONSTANS-LIKE 5 (COL5), HECATE 1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED (SYD). Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoter of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf. AN3-GR and wild-type (Col-0) plants were grown in vitro for 8 days and subsequently transferred to dexamethasone-containing medium for 8 hours. Developing leaves 1&2 of AN3-GR and wild-type plants were micro-dissected, and RNA was extracted. RNA from three biological repeats of dexamethasone-treated AN3-GR and dexamethasone-treated wild-type leaves was hybridized to Affymetrix ATH1 microarrays.
2014-09-09 | E-GEOD-42875 | biostudies-arrayexpress
Project description:Gene Expression changes in BMDCs stimulated with H. pylori vs. E. coli. The hypothesis tested was that the gene expression profile in BMDCs stimulated with H. pylori lysate will be less inflammatory than BMDCs stimulated with E. coli.
2013-06-14 | GSE44954 | GEO
Project description:The goals of this study are to compare the transcriptome profiling (RNA-seq) of tumor cell-derived exosome treated BMDCs to normal cell-derived exosome treaed BMDCs or untreated BMDCs to explore the differential regulated signaling pathways or cellular processes.
2021-01-04 | GSE155881 | GEO
Project description:The transcriptional coactivator ANGUSTIFOLIA 3 (AN3) stimulates cell proliferation during Arabidopsis leaf development, but the molecular mechanism is largely unknown. We show here that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR 2 (CRF2), CONSTANS-LIKE 5 (COL5), HECATE 1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED (SYD). Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoter of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.
2014-09-09 | GSE42875 | GEO
Project description:Fibroblasts usually mediate acute wound healing and long-term tissue remodeling with scarring in tissue injury. In myocardial infarction (MI), following a prolonged lack of oxygen supply, necrotized cardiomyocytes become replaced by secreted extracellular matrix proteins produced by fibroblasts. Dendritic cells (DCs) act as inflammatory cells and can migrate from the bone marrow to the infarct areas and infarct border areas to mediate collagen accumulation after MI, whereas trichostatin A (TSA) can regulate the apoptosis and proliferation of the fibroblasts and affect DCs functions under oxygen–glucose deprivation (OGD) conditions. In this study, we used proteomics to investigate the effects of TSA and bone marrow-derived dendritic cells (BMDCs) on NIH3T3 fibroblasts under OGD conditions. Results showed that the fatty acid degradation pathway was significantly upregulated in NIH3T3 cells under OGD conditions, and the fatty acid synthesis pathway was significantly downregulated in NIH3T3 cells treated with BMDCs conditioned media with TSA (BMDCs-CM[TSA]) under OGD conditions. Meanwhile, the BMDCs-CM(TSA) significantly decreased the levels of triglycerides and free fatty acids and mediated ten fatty acid metabolism-related proteins in the NIH3T3 cells under OGD conditions. Summarily, the proteomic analysis showed that TSA and BMDCs affect fatty acid metabolism in NIH3T3 cells under OGD conditions.
2024-05-21 | PXD021469 | Pride
Project description:Nitidine Chloride(NC) were found to enhance IL-10 production in LPS-stimulated Bone-marrow dendritic cells(BMDCs ) ,while at the same time inhibit pro-inflammatory cytokines production, such as TNF- α and IL-6. BMDCs were treated with NC or vehicle following LPS stimulation to find out the influence of NC on BMDCs that regulate cytokines expression. This study indicated that NC regulate numerous gene expression, thus influence IL-10 and pro-inflammatory cytokines production in LPS-treated BMDCs.
2017-08-05 | GSE102135 | GEO