Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Fabian Guendel

PROVIDER: E-MTAB-9522 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of small intestinal macrophages, neutrophils, CD103-CD11b+cDC and cryptopatch and ILF associated mononuclear phagocytes (CIA-MPh)

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. CIA-MPh expressed very high levels of lysozyme M (LysM), but they did not express Ly6G or CD64, normally associated with LysM-expressing neutrophils or macrophages, respectively. In order to understand the ontogeny and function of these newly identified MPh subset, we performed genome-wide transcriptional profiling of CIA-MPh and other cell types expressing LysM (i.e., neutrophils and macrophages) in the small intestine as well as of CD11b+ CD103- cDC2. Using Lyz2-GFP reporter mice, we developed a sorting strategy allowing us to highly purify neutrophils, macrophages, CD11b+ CD103- cDC2 and CIA-MPh. The RNA of each sample was extracted using the ImmGen protocol with phase lock tubes. The libraries were prepared using the SMARTer Ultra Low Input RNA kit (Clontech) according to the manufacturer’s instructions. The material was enriched for poly-A sequences and single-end Next Generation Sequencing was performed on a HiSeq 2500 machine (Illumina).

2020-11-24 | E-MTAB-9505 | biostudies-arrayexpress

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

Microarray analysis of WT ESAM+ and ESAM- cDC 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 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

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

Differential Peak Calling of ChIP-Seq Signals with Replicates with THOR

Project description:Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells in bone marrow by successive steps of lineage commitment and differentiation. Different DC subsets were identified based on phenotype, localisation and function: (i) classical DC (cDC) and plasmacytoid DC (pDC) are found in lymphoid organs and (ii) migratory tissue DC are spread throughout peripheral organs, including Langerhans cells, the cutaneous contingent of DC. We have developed a two-step culture system that recapitulates DC development in vitro (Felker et al., J. Immunol. 185, 5326-5335, 2010). In this system multipotent hematopoietic progenitors (MPP) progress into DC-restricted common DC progenitors (CDP) and further into the two major DC subsets cDC and pDC. We employed chromatin immunoprecipitation (ChIP) with deep sequencing (ChIP-seq) to determine the dynamics of H3K27ac occupancy in MPP, CMP, cDC and pDC. Histone modification H3K27ac and RNA-Seq in MPP, CDP, cDC and pDC

2016-08-03 | E-GEOD-73143 | biostudies-arrayexpress

Genomic expression analysis of human monocyte-derived DCs and monocytes

Project description:To identify the functional non-coding RNAs in human DC development, we explored the gene expression profiles during DC development from peripheral monocytes. Using RNA-seq, we identified many annotated lncRNAs with markedly altered expressions during human DC differentiation and maturation. RNA samples from human peripheral blood monocytes and monocyte-derived DCs were collected. RNAs from 3 donors were pooled together to form monocyte sample or DC sample and then these two samples were subjected to RNA-seq and analysis.

2014-05-02 | E-GEOD-54401 | biostudies-arrayexpress

RNA-seq of small intestinal macrophages, neutrophils, CD103-CD11b+cDC and cryptopatch and ILF associated mononuclear phagocytes (CIA-MPh)

Project description:RNA-seq of small intestinal macrophages, neutrophils, CD103-CD11b+cDC and cryptopatch and ILF associated mononuclear phagocytes (CIA-MPh)

| PRJEB40143 | ENA

Tissue-specific factors differentially regulate the expression of antigen-processing enzymes during dendritic cell ontogeny

Project description:Dendritic cells (DC) form a collection of antigen-presenting cells that are distributed throughout the body. Conventional DC (cDC) which include the cDC1 and cDC2 subsets, and plasmacytoid DC (pDC) constitute the two major ontogenically distinct DC populations. The pDC complete their differentiation in bone-marrow (BM) while the cDC subsets derive from pre-committed bone-marrow (BM) precursors, the pre-cDC, that seed lymphoid and non-lymphoid tissues where they further differentiate into mature cDC1 and cDC2. Within different tissues, cDC express distinct phenotype and function. Notably cDC in the thymus are exquisitely efficient at processing and presenting antigens in the class II pathway, while in the spleen they do so only upon maturation induced by danger signals. To appraise this functional heterogeneity, we examined the regulation of the expression of distinct antigen-processing enzymes during DC ontogeny. We analyzed the expression of cathepsin S (CTSS), cathepsin L (CTSL) and thymus specific serine protease (TSSP), three major antigen-processing enzymes regulating class II presentation in cDC, by DC BM precursors and immature and mature cDC from spleen and thymus. We found that pre-cDC in the BM express relatively high levels of these different proteases. Then, their expression is modulated in a tissue-specific and subset–specific manner with immature and mature thymic cDC expressing overall higher levels than immature splenic cDC. On the other hand, TSSP expression level is selectively down-regulated in spleen pDC while CTSS and CTSL are both increased in thymic and splenic pDC. Hence tissue-specific factors program the expression levels of these different proteases during DC differentiation thus conferring tissue-specific function to the different DC subsets.

2020-01-29 | GSE144421 | GEO

Differential Peak Calling of ChIP-Seq Signals with Replicates with THOR

Project description:Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells in bone marrow by successive steps of lineage commitment and differentiation. Different DC subsets were identified based on phenotype, localisation and function: (i) classical DC (cDC) and plasmacytoid DC (pDC) are found in lymphoid organs and (ii) migratory tissue DC are spread throughout peripheral organs, including Langerhans cells, the cutaneous contingent of DC. We have developed a two-step culture system that recapitulates DC development in vitro (Felker et al., J. Immunol. 185, 5326-5335, 2010). In this system multipotent hematopoietic progenitors (MPP) progress into DC-restricted common DC progenitors (CDP) and further into the two major DC subsets cDC and pDC. We employed chromatin immunoprecipitation (ChIP) with deep sequencing (ChIP-seq) to determine the dynamics of H3K27ac occupancy in MPP, CDP, cDC and pDC. Additionally, we monitored changes in gene expression in MPP, CDP, cDC and pDC by RNA-seq.

2016-08-03 | GSE73143 | GEO

Mice bone marrow-derived dendritic cells (BMDC) infected by Listeria: cell lysate proteome and PTMs

Project description:In this study, we aimed to determine the role of EVs derived from Lm-infected DCs in the innate response, and the potential role of HDAC6 in DEV loading under these conditions. Ourresults show that Lm infection induced an elevated production of DEVs. Lm infection also altered protein sorting. Interestingly, HDAC6 deletion altered DEV protein sorting, although it did not affect acetylation of DEV-loaded proteins. However, protein ubiquitination was severely altered. Here, we show that the protein content of dendritic cells (DCs) and their secreted EVs (DEVs) vary dramatically during Lm infection. The proteomic profiles of DC and DEV differ depending on whether HDAC6 is expressed or not.

2022-08-30 | PXD033995 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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