Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

46 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from Ly6G+ and Ly6G- dendritic cells (DC)

ABSTRACT: To investigate the functional properties of Ly6G+ DC, we employed GeneChip analysis to compare the gene expression profiles between Ly6G+ DC and Ly6C- DC. Crude bone marrow (BM) cells prepared from C57BL/6 mice were cultured in the presence of GM-CSF. On day 6, CD11c+/MHC II+/Ly6G+ cells and CD11c+/MHC II+/Ly6G- cells were simultaneously sorted from the same cultures by FACSAria. Total RNA were extracted and hybridized on Affymetrix microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Hironori Matsushima

PROVIDER: E-GEOD-28408 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Neutrophil differentiation into a unique hybrid population exhibiting dual phenotype and functionality of neutrophils and dendritic cells.

Matsushima Hironori H Geng Shuo S Lu Ran R Okamoto Takashi T Yao Yi Y Mayuzumi Nobuyasu N Kotol Paul F PF Chojnacki Benjamin J BJ Miyazaki Toru T Gallo Richard L RL Takashima Akira A

Blood 20130110 10

Neutrophils have been reported to acquire surface expression of MHC class II and co-stimulatory molecules as well as T-cell stimulatory activities when cultured with selected cytokines. However, cellular identity of those unusual neutrophils showing antigen presenting cell (APC)-like features still remains elusive. Here we show that both immature and mature neutrophils purified from mouse bone marrow differentiate into a previously unrecognized "hybrid" population showing dual properties of both ...[more]

PMID: 23305731

Similar Datasets

Mouse lung CD103+ and CD11b-high dendritic cell (DC) subsets

Project description:Mouse lung CD11c+ dendritic cells are composed of 2 major DC subsets, the CD103+CD11b-low/intermediate DC (CD103+ DC) and the CD11b-highCD103- DC (CD11b-high DC). These 2 subsets are functionally distinct. Comparison of their functions showed CD103+ DC Microarray analysis was performed to compare the gene expression profiles of the 2 lung DC subsets in naÃ¯ve mice. Perfused lungs from 6-8-week naÃ¯ve BALB/cByJ mice were pooled and digested with collagenase D. CD11c+ cells were selected by anti-CD11c magnetic microbeads (Miltenyi) and stained by fluorochrome-conjugated mAb against I-A, CD103, CD11b, and CD11c plus 7-

2010-03-24 | E-GEOD-17322 | biostudies-arrayexpress

Gene expression profile in CD11c+ splenic dendritic cells and CD11c+CD103+ dendritic cells from mesenteric lymph nodes (MLN) of mice with DC-specific targeting of TGFBR2

Project description:Transcriptome analysis of dentritic cells from the spleen (CD11c+) or MLN (CD11c+CD103+) of mice with DC-specific deletion of TGFBR2 gene, or their control littermates. TRGFR2 gene was deleted in dendritic cells using Cre/lox approach. Mice with this deletion develop spontaneous multi-organ autoimmune inflammation and die by 15 weeks of age. Splenic CD11c+ Dc were isolated by magetic cell sorting. MLN CD11c+CD103+ DC were flow sorted. RNA was isolated using RNAqueous-Micro kit (Ambion) and analyzed using Affymetrix Mouse Exon 1.0 ST Array

2012-07-25 | E-GEOD-39651 | 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

ChIP-Seq (H3K4me3, H3K27me3) of steady-state splenic classical dendritic cells from wild type, germ-free and IFNAR knockout mice

Project description:The epigenetic state of splenic cDCs from Wild Type (WT) mice, Germ Free (GF) and mice deficient for the Ifnar1 gene (IFNAR) was characterized by analyzing the occupancy of a major activating histone mark (H3K4me3) and a major repressive histone mark (H3K27me3). Splenic cDCs (CD3- CD19- CD45+ MHC-II+ CD11c+) were sorted to high purity by flow cytometry and subject to chromatin immunoprecipitation.

2018-06-30 | E-MTAB-5234 | biostudies-arrayexpress

RNA-Seq of steady-state and LPS stimulated splenic classical dendritic cells from wild type, germ-free and IFNAR knockout mice

Project description:The transcriptome of splenic classical dendritic cells (cDCs) (CD3- CD19- CD45+ MHC-II+ CD11c+) was compared in Wild Type (WT) mice, Germ Free (GF) mice and mice deficient for the Ifnar1 gene (IFNAR). Cells were isolated and sorted by flow cytometry to high purity. The cells were stimulated ex vivo with PBS or LPS. The results show remarkable similarities between the transcriptome of splenic cDCs in GF and IFNAR mice.

2018-06-30 | E-MTAB-5190 | biostudies-arrayexpress

Small RNA Solexa sequencing of mouse CD11c+Ia high and CD11c+Ia low cells

Project description:We applied Illumina massively parallel signature sequencing to identify miRNomes in CD11c+Ia high and CD11c+Ia low cells.The miRNomes of these DC subsets will contribute to investigate the significance of miRNAs in DC immunobiology. Examination of miRNome in CD11c+Ia high and CD11c+Ia low cells . All two mouse cell types.

2015-06-16 | E-GEOD-51574 | 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

2021-03-21 | PXD023581 | Pride

Microarray analysis of committed cDC progenitors

Project description:Analysis of stage-specific gene expression in Zbtb46GFP/+ pre-CD8 DCs, pre-CD4 DCs, CD24 cDCs and CD172a cDCs Bone Marrow and Splenocytes were harvested from 8-10 littermate Zbtb46GFP/+ mice and sorted to >95% purity on the FACS AriaFusion.

2015-06-08 | E-GEOD-66565 | biostudies-arrayexpress

Microarray analysis of WT and Notch2-deficient classical DC subsets

Project description:Defense against attaching and effacing (A/E) bacteria requires the sequential generation of IL-23 and IL-22 to induce protective mucosal responses. While the critical source of IL-22 has been identified as CD4+ and Nkp46+ innate lymphoid cells (ILCs), the precise source of IL-23 is unclear. Here, we use genetic techniques to deplete specific classical dendritic cell (cDC) subsets and analyze immunity to the A/E pathogen Citrobacter rodentium. We find that Zbtb46+ cDCs, and specifically Notch2-dependent intestinal CD11b+ cDCs, but not Batf3-dependent CD103+ cDCs, are required for IL-23 production and immunity against C. rodentium. Notch2 controls cDC differentiation at a terminal step mediated by lymphotoxin signaling. Importantly, these results provide the first demonstration of a non-redundant function of CD11b+ cDCs in vivo. Analysis of Notch2-dependent genes in CD11b+ and DEC205+ splenic classical DC subsets. Splenocytes were harvested from littermate WT Notch2 f/f C57Bl/6 or Notch2 CD11c-cre C57Bl/6 mice and DC subsets sorted to >95% purity on the FACSAriaII.

2013-06-01 | E-GEOD-45681 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data