Microarray analysis of WT and Batf3-/- CD8alpha dendritic cells from C57BL/6 spleen
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Kenneth Murphy
PROVIDER: E-GEOD-40647 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Batf3 regulates key CD8alpha DC-specific genes.
2012-09-30 | GSE40647 | GEO
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 differentially expressed genes in ESAM+ and ESAM- CD11b+ and DEC205+ splenic classical DC subsets. Splenocytes were harvested from WT C57Bl/6 or WT Cx3cr1-gfp mice and cDC subsets sorted to >95% purity on the FACSAriaII.
2013-06-01 | E-GEOD-45679 | biostudies-arrayexpress
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
Project description:The dendritic cell (DC)-derived chemokine CCL17, a ligand of CCR4, has been shown to promote various inflammatory diseases such as atopic dermatitis, atherosclerosis, and inflammatory bowel disease. Under steady state conditions, and even after systemic stimulation with lipopolysaccharide, CCL17 is not expressed in resident splenic DC as opposed to CD8-CD11b+ lymph node (LN) DC, which produce large amounts of CCL17, in particular after maturation. Upon systemic NKT cell activation through alpha-galactosylceramide stimulation, however, CCL17 can be upregulated in both CD8- and CD8+ splenic DC subsets and enhances cross-presentation of exogenous antigens. Based on genome wide expression profiling, we now show that splenic DC are susceptible to Interferon-gamma (IFNgamma) mediated suppression of CCL17, whereas LN DC are much less responsive to IFNgamma and downregulate the IFNgamma receptor. Under inflammatory conditions, particularly in the absence of IFNgamma signaling in IFNgamma receptor deficient mice, CCL17 expression is strongly induced in a major proportion of splenic DC by the action of granulocyte-macrophage colony stimulating factor (GM-CSF) in concert with interleukin (IL)-4. Our findings demonstrate that the local cytokine milieu and differential cytokine responsiveness of DC subsets regulate lymphoid organ specific immune responses at the level of chemokine expression. 15 h after pretreatment with 100 µg LPS, spleens and LN (MLN and PLN) from CCL17E/+ mice were harvested and DC-enriched cell suspensions of the respective organs were stained for NK1.1, CD8alpha, CD11c and CD11b. For isolation of LN DC, NK1.1-CD8alpha-CD11c+CD11b+ cells expressing CCL17/EGFP were sorted (FACSAria). Splenic DC were sorted in parallel from the same mice, but only CCL17/EGFP-negative cells expressing the same markers were selected. After the sort, cells were immediately lysed in Trizol (Invitrogen) before storage at -80°C for RNA isolation.
2013-09-19 | E-GEOD-43456 | biostudies-arrayexpress
Project description:We identified DCIR2+DCs but not DEC205+DCs as able to induce peripheral T cell tolerance in pre-diabetic autoimmune NOD mice. To determine what distinct genetic programs are elicited in the auto-reactive CD4 T cells early after stimulation by these two DC subsets, we utilized adoptive transfer of BDC2.5 CD4 T cells into NOD mice, which were then given chimeric antibody to deliver the beta-cell specific antigen to either DCIR2+DCs or DEC205+DCs, leading to BDC2.5 CD4 T cell specific stimulation in vivo. The analysis shows that the negative transcriptional factor Zbtb32 (ROG) is up-regulated more in BDC2.5 CD4 T cells after stimulated with a antigen via DCIR2+DCs presentation, compared with DEC205+DCs, suggesting the involvement of Zbtb32 in DCIR2+DCs-mediated auto-reactive T cell tolerance in disease ongoing NOD mice. The BDC2.5 CD4 T cells after 14 hour of injection with a 100 ng of anti-DCIR2-BDC, anti-DEC205-BDC antibody, or PBS as a control to NOD mice, were sorted by BD FACSAria and their expression profile was analyzed using Affymetrix chips. NOD mice with transferred BDC2.5 T cell were injected with 100 ng of anti-DCIR2-BDC (NOD_DCIR2-BDC), anti-DEC205-BDC antibody (NOD_DEC-BDC), or PBS (NOD_PBS) as a control. After 14 hours, BDC2.5 CD4 T cells were sorted by BD FACSAria and their expression profile was analyzed using Affymetrix microarray chips. Each sample has a biological duplicate. Raw data were preprocessed with the RMA algorithm in Partek, and averaged expression values were used for analysis.
2015-07-01 | E-GEOD-69554 | biostudies-arrayexpress
Project description:Bone marrow cells were isolated from wild type and Tbx21 knockout mice. iNK (Lin- NK1.1+ CD11b- CD27+) and mNK1 (Lin- NK1.1+ CD11b+ CD27+) were sorted from WT and Tbx21 KO mice. mNK2 (Lin- NK1.1+ CD11b+ CD27-) were sorted from WT mice only, since these cells are not present in Tbx21 KO mice.
2019-03-20 | GSE122874 | GEO
Project description:We investigated the transcriptomes of monocytes in a variety of mouse tissue. Monocytes were were identified as CD45+ Lin(CD3ε, TCR-β, CD19, B220, NK1.1, Ter119, Siglec F, Ly6G)- CD11b+ Ly6Chi CD64- MHCII- and their RNA was sequenced on the Illumina HiSeq2500PE
2021-02-05 | E-MTAB-10039 | biostudies-arrayexpress
Project description:Innate immune responses are critical for mucosal immunity. Here we describe an innate lymphocyte population, iCD8a cells, characterized by expression of CD8a homodimers. iCD8a cells exhibit innate functional characteristics such as the capacity to engulf and kill bacteria. Development of iCD8a cells depends on expression of interleukin-2 receptor g chain (IL-2Rgc), IL-15, and the major histocompatibility complex (MHC) class Ib protein H2-T3, also known as the thymus leukemia antigen or TL. While lineage tracking experiments indicated that iCD8a cells have a lymphoid origin, their development was independent of the transcriptional suppressor Id2, suggesting these cells do not belong to the family of innate lymphoid cells. Finally, we identified cells with a similar phenotype in humans, which were profoundly depleted in newborns with necrotizing enterocolitis. These findings suggest a critical role of iCD8a cells in immune responses associated with the intestinal epithelium. Three different populations of immune cells present in the intestine epithelium of RAG-2 deficient mice were compared at the transcriptome level. These populations were defined as: a. CD45+CD8alpha+ (iCD8a cells), b. NKp46+NK1.1+ (group 1 ILC), and c.CD45+CD8alpha-CD11b+ (myeloid cells). High quality RNA was sequenced at the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core using an Illumina HiSeq 2500. RAN data alignment was performed by top hat, followed by gene quantification (FPKM) using Cufflinks. Additional read count was generated using HTSeq. Differential expression analysis was carried out using both FPKM and read count-based methods. Pathway and network analyses were performed using Ingenuity.
2014-11-27 | E-GEOD-63674 | biostudies-arrayexpress
Project description:We isolated splenic NK cells and cultured them for 3 days in 100 ng/ml IL-15. Next, we stimulated the cells with plate-bound anti-NK1.1 for 6 hours and sorted YFP+ (IFNg+) and YFP- (IFNg-) populations. We then performed gene expression profiling analysis using data obtained from RNA-seq from unstimulated, YFP+ or YFP- NK cells.
2023-08-01 | GSE227863 | GEO
Project description:Mice were weaned onto standard RM1 diet or onto a highly palatable obesogenic diet (824018 – ‘45% AFE fat) supplemented with condensed milk. After 12 weeks, mice were killed, and liver NK cells (Lin- NK1.1+ CD49a- CD49b+) or ILC1 (Lin- NK1.1+ CD49a+ CD49b-) were sorted. Total RNA was extracted from sorted cells, cDNA generated and RNASeq performed.
2019-03-13 | GSE122828 | GEO