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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of lung myeloid cells from WT and Ptgs2-cKO mice

ABSTRACT: To investigate the role of the COX-2-dependent lung fibroblast program in reprogramming lung myeloid cells, we generated fibroblast-targeted Ptgs2 conditional knockout mice by crossing Pdgfra-Cre mice with Ptgs2flox/flox mice. Then we isolated two primary types of lung resident DCs-CD103+ conventional DC (cDC1) and CD11b+ conventional DC (cDC2), and lung monocytes from WT and Ptgs2 cKO mice by fluorescence-activated cell sorting and performed RNA sequencing.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Zheng Gong

PROVIDER: E-MTAB-11888 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single-cell transcriptional profiles of lung CD45+ immune cells from WT and Ptgs2-cKO mice

Project description:To better understand the role of the COX-2-dependent lung fibroblast program in modulating the lung immune microenvironment, we generated fibroblast-targeted Ptgs2 conditional knockout (cKO) mice by crossing Pdgfra-Cre mice with Ptgs2flox/flox mice. Then we determined how Ptgs2 deficiency in CD140a+ fibroblasts alters the lung immune microenvironment by performing single-cell RNA sequencing on lung CD45+ immune cells from WT and Ptgs2-cKO mice.

2022-07-19 | GSE206449 | GEO

RNA-seq of Mus musculus BM-DCs upon stimulation by lung fibroblast conditioned medium or purified PGE2

Project description:To comprehensively understand how dendritic cells (DCs) are reprogrammed by lung fibroblasts- and their derived COX-2/PGE2, we employed lung fibroblasts isolated from WT or Ptgs2-/- mice, and collect their conditioned medium (CM) to stimulate the ex vivo cultured bone marrow (BM)-derived DCs (BM-DCs), with the PGE2 treatment as a control. After the treatment, BM-DCs were harvested for RNA extraction and the transcriptional profiles were analyzed by RNA sequencing (RNA-seq).

2022-07-19 | E-MTAB-11873 | biostudies-arrayexpress

Nano LC-MS/MS DDA mass spectrometry profiling of I-Ab MHCII immunopeptidome eluted from B6 mice on normal and high fructose/high fat (HFHF) diet

Project description:In Dendritic cells (DC), the MHC II eluted immunopeptidome reflects the antigenic composition of the microenvironment. Proteins are transported and processed into peptides in endosomal MHC II compartments through autophagy or phagocytosis; extracellular peptides can also directly bind MHC II proteins at the cell surface. Altogether, these mechanisms allow DC to sample both the intra and extracellular environment. With an increase in mass spectrometry sensitivity and accuracy, we can now finally tackle important questions on the nature and plasticity of the MHC-II immunopeptidome in health and disease. Presented epitopes, neoepitopes, and PTM-modified epitopes can be quantitatively and qualitatively analyzed to provide a comprehensive picture of DC role in immunosurveillance. To determine whether the redox metabolic conditions induce an altered spectrum of presented peptides, we eluted immunoaffinity-purified I-Ab from conventional dendritic cells isolated from B6 mice on normal or high fat/high fructose (HFHF) diet and analyzed MHC-II-associated peptides by nano LC-MS/MS using data-dependent (DDA) acquisition approaches. Our results show that the environment-driven lipotoxicity and glucotoxicity induced an MHC-class-II immunopeptidome enriched in peptides derived from proteins involved in cellular metabolism, oxidative phosphorylation, and responses to redox mediated cellular stress. The quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in mice subjected to a diet rich in saturated fat and carbohydrates, which in turn, could be responsible for inducing a low-grade chronic inflammation in several organs including nonalcoholic steatohepatitis.

2022-08-22 | PXD026068 | Pride

Batf3 maintains Irf8 autoactivation for commitment of a novel clonogenic progenitor of CD8+DCs

Project description:The transcription factors Batf3 and IRF8 are required for development of CD8α+ conventional dendritic cells (cDCs), but the basis for their actions was unclear. Here, we identify two novel Zbtb46+ progenitors that separately generate CD8α+ and CD4+ cDCs and arise directly from the common DC progenitor (CDP). Irf8 expression in the CDP depends on prior PU.1-dependent autoactivation, and specification of pre-CD8 DC progenitors requires IRF8 but not Batf3. However, upon pre-CD8 DC specification, Irf8 autoactivation becomes Batf3-dependent at a CD8α+ cDC-specific enhancer containing multiple AP1-IRF composite elements (AICEs) within the Irf8 superenhancer. CDPs from Batf3-/- mice that specify toward pre-CD8 DCs fail to complete CD8α+ cDC development due to decay of Irf8 autoactivation, and divert to the CD4+ cDC lineage. Examination of histone modifications (H3K27ac and H3K4me1) and 2 transcription factors (Batf3 and Irf8) and the p300 co-factor binding in 3 different dendritic cell subsets

2015-06-08 | E-GEOD-66899 | biostudies-arrayexpress

Characterization of I-Ab MHCII immunopeptidome eluted from control and obese (Ob/Ob) mice (2)

Project description:In Dendritic cells (DC), the MHC II eluted immunopeptidome reflects the antigenic composition of the microenvironment. Proteins are transported and processed into peptides in endosomal MHC II compartments through autophagy or phagocytosis; extracellular peptides can also directly bind MHC II proteins at the cell surface. Altogether, these mechanisms allow DC to sample both the intra and extracellular environment. With an increase in mass spectrometry sensitivity and accuracy, we can now finally tackle important questions on the nature and plasticity of the MHC-II immunopeptidome in health and disease. Presented epitopes, neoepitopes, and PTM-modified epitopes can be quantitatively and qualitatively analyzed to provide a comprehensive picture of DC role in immunosurveillance. To determine whether the redox metabolic conditions induce an altered spectrum of presented peptides, we eluted immunoaffinity-purified I-Ab from conventional dendritic cells isolated from control B6 or obese Ob/Ob mice, and analyzed MHC-II-associated peptides by LC/MS/MS using combined data-dependent (DDA) and data-independent acquisition (DIA) approaches. We analyzed the DIA data by employing a reference spectral library consisting of all peptides identified by database matching in the pool of spectra from combined DDA dataset, thus allowing a direct label-free quantitation of relative abundances between the two sample categories. The quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in obese mice.

2021-03-21 | PXD018783 | Pride

Single cell RNA sequencing of small intestinal dendritic cells from C57BL/6, RORgt-/- and RORgt-Cre x Ltb-flox mice

Project description:Cryptopatches (CP) and isolated lymphoid follicles (ILF) are evolutionary ancient lymphoid structures found in the intestines of all vertebrates. These structures are demarcated by a poorly characterised subset of mononuclear phagocytes (MPh), called CP/ILF-associated (CIA)-MPh. We could demonstrate that CIA-MPh derive from a pre-DC from the bone marrow and thus are boafide dendritic cells. We called these newly identified cDC cells : cryptopatch and ILF associated dendritic cells (CIA-DC). To obtain unbiased insights into how CIA-DC are integrated into the intestinal cDC landscape, we performed single cell RNA-sequencing (scRNA-seq) of purified CD45+ CD64- I-A/I-E+ CD11chigh cells from C57BL/6 mice using the 10X Genomics droplet-based technology. Finally, to study the role of ILC3 in the final differentiation of CIA-DC, we performed single cell RNA-sequencing (scRNA-seq) of cDC from Rorc(γt)-/- and Ltb∆ILC3,T mice, using the 10X Genomics droplet-based technology.

2020-11-24 | E-MTAB-9522 | biostudies-arrayexpress

Feedback amplification of fibrosis through matrix stiffening and COX-2 suppression

2010-07-15 | GSE22011 | GEO

Microarray analysis of WT and L-Myc-deficient DC subsets

Project description:Analysis of L-Myc-dependent genes in pDCs and classical DC subsets with and without stimulation. Splenocytes were harvested from C57BL/6 wild-type (WT) or 10 generation C57BL/6 backcrossed Mycl1-gfp/gfp (LmycKO) mice and DC subsets sorted to >95% purity on the FACSAriaII.

2013-12-14 | E-GEOD-53312 | biostudies-arrayexpress

Characterization of I-Ab MHCII immunopeptidome eluted from control and obese (Ob/Ob) mice using a combination of data-dependent (DDA) and data-independent acquisition (DIA) nanoLC mass spectrometry

Project description:In Dendritic cells (DC), the MHC II eluted immunopeptidome reflects the antigenic composition of the microenvironment. Proteins are transported and processed into peptides in endosomal MHC II compartments through autophagy or phagocytosis; extracellular peptides can also directly bind MHC II proteins at the cell surface. Altogether, these mechanisms allow DC to sample both the intra and extracellular environment. With an increase in mass spectrometry sensitivity and accuracy, we can now finally tackle important questions on the nature and plasticity of the MHC-II immunopeptidome in health and disease. Presented epitopes, neoepitopes, and PTM-modified epitopes can be quantitatively and qualitatively analyzed to provide a comprehensive picture of DC role in immunosurveillance. To determine whether the redox metabolic conditions induce an altered spectrum of presented peptides, we eluted immunoaffinity-purified I-Ab from conventional dendritic cells isolated from control B6 or obese Ob/Ob mice, and analyzed MHC-II-associated peptides by LC/MS/MS using combined data-dependent (DDA) and data-independent acquisition (DIA) approaches. We analyzed the DIA data by employing a reference spectral library consisting of all peptides identified by database matching in the pool of spectra from combined DDA dataset, thus allowing a direct label-free quantitation of relative abundances between the two sample categories. The quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in obese mice.

2021-03-21 | PXD023581 | Pride

Feedback amplication of fibrosis through matrix stiffening and COX-2 suppression

Project description:We tested the hypothesis that increasing matrix stiffness on which normal human lung fibroblasts are grown promotes the expression of a fibrogenic cellular transcriptomic program. Keywords: Human lung fibroblast, matrix stiffness, PTGS2, COX-2, Prostaglandin E2 Total RNA extracted from normal human lung fibroblasts from 3 human subjects and separately grown on 5 discrete matrix stiffness conditions: 100, 400, 1600, 6400, 25600 Pascals.

2010-07-15 | E-GEOD-22011 | biostudies-arrayexpress

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