Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-19187E-GEOD-19182
PROVIDER: PRJNA123741 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE19182: Gene expression profiling of differentiated HNECs stimulated by IL4, IL13, IFNalpha, IFNbeta, IFNgamma and controls GSE19187: Nasal epithelium gene expression profiling in child respiratory allergic disease Refer to individual Series
2012-01-05 | E-GEOD-19190 | biostudies-arrayexpress
Project description:Gene expression profiling of differentiated HNECs stimulated by IL4, IL13, IFNalpha, IFNbeta, IFNgamma and controls
2015-07-27 | E-GEOD-19182 | ExpressionAtlas
Project description:Transcriptional profiling of HIV-1 infected and that of IFNbeta, IFNgamma or LPS stimulated human monocyte derived macrophages.
2009-09-01 | E-MEXP-2032 | biostudies-arrayexpress
Project description:Excessive inflammation within the central nervous system is injurious, but an immune response is also required for its repair. Macrophages are versatile cells that adopt different properties depending upon their microenvironment. Exposing macrophages to interleukin-4 and -13 (IL4/IL13) has incurred interest for their reparative properties. Unexpectedly, while macrophages exposed to the classic pro-inflammatory signals (interferon-γ/lipopolysaccharide, IFN/LPS) killed neurons and oligodendrocytes in culture, the addition of LPS to IL4/IL13-treated macrophages profoundly elevated IL10, repair metabolites (lactate, ornithine), glucose metabolism and the oligodendrocyte-trophic heparin-binding epidermal growth factor (HBEGF); cells did not display pro-inflammatory or neurotoxic features. In mice with spinal cord demyelination, locally-applied IL4/IL13 was insufficient to alter responses beyond controls; remarkably, the LPS/IL4/IL13-treated animals significantly increased lesional phagocytic macrophages/microglia, lactate and HBEGF levels, oligodendrogenesis and remyelination. We report a remarkably reparative state of macrophages that is unexpectedly generated by the integration of pro- (LPS) and anti- (IL4/IL13) inflammatory activation cues.
2019-09-06 | PXD015021 | Pride
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived IL4/IL13 treated BMDMs transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods. Methods: BMDMs mRNA profiles of 8 weeks old wild-type (WT) mice were generated, stimulated with IL4/IL13, IL4/IL13+ TNF or TNF, deep sequenced, in triplicate, using Illumina NovaSeq 6000 platform. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9). Conclusions: Our study represents the first detailed analysis of IL4/IL13 or IL4/IL13+TNF stimulated BMDMs, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2021-05-04 | GSE169348 | GEO
Project description:In this study, we explored gene expression profiles of IL-3+IL-33-stimulated BMBAs treated with difamilast, a highly selective PDE4B inhibitor. We identified that difamilast-treated basophils showed downregulated expression of inflammaory mediators including Il4, Il6 and Il13.
2023-10-11 | GSE234541 | GEO
Project description:In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of human nasal epithelial cells (HNECs) cultured under air-liquid interface (ALI) conditions until differentiated and then stimulated with PM2.5 (100 μg/ml) for 24 hours.
2023-09-25 | GSE243618 | GEO
Project description:Hypoxia-inducible factor 1-alpha (HIF1a) is a basic helix-loop-helix PAS domain-containing protein, and is considered as the master transcriptional regulator of cellular response to hypoxia and inflammatory stimuli. Studies over the year have demonstrated that HIF1a play a critical role in innate immune cell response to infection and injury. Here we isolated bone marrow of 3 mice per group (Lyz2cre and Lyz2cre:HIF1aFl/Fl) and differentiated into macrophages by culturing them in M-CSF containing media. These cells were stimulated with 100ng/ml LPS, 10ng/ml IFNgamma, 10ng/ml IL4 or 10ng/ml IL10 for 18 hours. Total RNA was isolated and subjected to RNAseq analyses.
2021-03-05 | GSE131364 | GEO
Project description:The experiments were done using an Orbitrap Fusion or an Orbitrap Fusion Lumos mass spectrometer. Multiplexing was achieved using either TMT10 or TMT11 reagents and the SPS-MS3 method. Basic pH reversed-phase chromatography (bRPLC) was used for off-line pre-fractionation; 12 fractions were analyzed for proteome mappings (PMID: 26700037) and 24 fractions plus a phosphotyrosine-enriched sample for phosphoproteome mappings (PMID: 31606085). Phosphoproteome mappings were done using both HCD fragmentation with Orbitrap fragment ion detection and CID fragmentation with ion trap fragment ion detection (PMID: 29487189, PMID: 31606085). If multiple TMT sets were required to analyze all samples from an experiment two bridge channels pooled from all samples was used to connect the data from the individual TMT sets (PMID: 28892078).
Five proteomics experiments are described in the paper:
(i) 1. Quantitative proteomics of fully polarized macrophages after 4 days of treatment with IL4 or IFNgamma/LPS to determine global proteome landscape of fully polarized THP-1-derived M1-type versus M2a-type macrophages:
Proteome mapping on Orbitrap Fusion (one TMT set)
RAW files: Marneros_4DayTreatment_proteome_fraction01 to ...fraction12
8 samples
Labeling: PMA.1 (126), PMA.2 (127n), IL4.1 (127c), IL4.2 (128n), ILJQ1.1 (128c), ILJQ1.2 (129n), IFNgamma.1 (129c), IFNgamma.2 (130n)
(ii) Time-course quantitative proteomics during the first 24 hours after induction of macrophage polarization in THP-1-derived macrophages to identify protein changes associated with M1-type (IFNgamma/LPS-induced) versus M2a-type (IL-4-induced) polarization:
Proteome mapping on Orbitrap Fusion (three TMT sets: set01, set02, set03)
RAW files:
Marneros_timecourse_proteome_TMTset01_fraction01 to ...fraction12
Marneros_timecourse_proteome_TMTset02_fraction01 to ...fraction12
Marneros_timecourse_proteome_TMTset03_fraction01 to ...fraction12
22 samples
Labeling:
set01; bridge 1 (126), PMA 0min (127n), PMA 10min (127c), PMA 30min (128n), PMA 1h (128c), PMA 2h (129n), PMA 4h (129c), PMA 8h (130n), PMA 24h (130c), bridge 2 (131n)
set02; bridge 1 (126), IL4 10min (127n), IL4 30min (127c), IL4 1h (128n), IL4 2h (128c), IL4 4h (129n), IL4 8h (129c), IL4 24h (130n), IFN 10min (130c), bridge 2 (131n)
set03; bridge 1 (126), IFN 30min (127n), IFN 1h (127c), IFN 2h (128n), IFN 4h (128c), IFN 8h (129n), IFN 24h (129c), bridge 2 (131n)
(iii) Time-course quantitative phosphoproteomics during the first 24 hours after induction of macrophage polarization in THP-1-derived macrophages to identify phosphorylation events associated with M1-type (IFNgamma/LPS-induced) versus M2a-type (IL-4-induced) polarization (same time points as in group 2):
Phosphoproteome mapping on Orbitrap Fusion (three TMT sets: set01, set02, set03)
RAW files:
Marneros_timecourse_phospho_TMTset01_fraction01 to ...fraction06, ...fraction08 to ...fraction24, ...pY
Marneros_timecourse_phospho_TMTset02_fraction01 to ...fraction12, ...fraction16 to ...fraction24, ...pY
Marneros_timecourse_phospho_TMTset03_fraction01 to ...fraction24, ...pY
The following RAW files gave no phosphopeptide quantifications (they are no included in the group of provided RAW files): set01_fraction07, set02_fraction13, set02_fraction14, set02_fraction15.
22 samples
Labeling: as in (ii)
(iv) Quantitative proteomics to assess the effects of the B-Raf inhibitor GDC-0879 or of the MEK inhibitor trametinib on IL-4-induced M2-type polarization and IFNgamma/LPS-induced M1-type polarization on THP-1-derived macrophages after 24 hours of treatment:
Proteome mapping on Orbitrap Fusion (one TMT set)
RAW files: Marneros_BRAF_inhibitor_proteine_fraction01 to ...fraction12
11 samples
Labeling: IL4 1 (131c), IL4 2 (127n), IL4+GDC 1 (131n), IL4+GDC 2 (128n), IL4+TRAM 1 (130c), IL4+TRAM 2 (129n), IFNgamma+LPS 1 (130n), IFNgamma+LPS 2 (127c), IFNgamma+LPS+TRAM 1 (126), IFNgamma+LPS+TRAM 2(129c), IFNgamma+LPS+GDC (128c)
(v) Quantitative phosphoproteomics to assess the effects of the B-Raf inhibitor GDC-0879 on IL-4-induced M2-type polarization and IFNgamma/LPS-induced M1-type polarization on THP-1-derived macrophages after 24 hours of treatment:
Phosphoproteome mapping on Orbitrap Fusion Lumos (one TMT set)
RAW files: Marneros_BRAF_inhibitor_phospho_fraction01 to ...fraction24, ...pY
7 samples
Labeling: IL4 1 (131c), IL4 2 (127n), IL4+GDC 1 (130n), IL4+GDC 2 (128n), IFNgamma+LPS 1 (128c), IFNgamma+LPS 2 (127c), IFNgamma+LPS+GDC (130c)
2019-12-10 | MSV000084672 | MassIVE
Project description:This SuperSeries is composed of the following subset Series: GSE17914: IL13 and CCL2 Drive Disease in an Inflammatory Subset of Scleroderma [cGVHD] GSE24403: IL13 and CCL2 drive disease in an inflammatory subset of Scleroderma [IL13] GSE24409: IL13 and CCL2 drive disease in an inflammatory subset of Scleroderma [IL4] Refer to individual Series
2011-06-30 | E-GEOD-24410 | biostudies-arrayexpress