Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of dendritic cell subsets

ABSTRACT: Comparison of cDC1, cDC2, mcDC transcriptome Conventional dendritic cells (cDCs) are classically subdivided in two subsets, named cDC1 and cDC2. We demonstrated that mcDC are a new subset of cDCs. To understand their transcriptomic relatedness, we perform a RNA sequencing on cDC1, cDC2 and mcDCs sorted from mouse spleens. We demonstrate that cDC1, cDC2 and mcDCs all cluster independently in a PCA analysis and an unbiased hierarchical cluster analysis reveals unique gene profile for all three cDC subsets. As mcDC cluster slightly more towards cDC1 than cDC2, we next aimed to more closely examine the transcriptomic relatedness between mcDC and cDC2. We compared the DC subsets gene expression signatures based on a selected gene set known to define cDC2. Both the PCA and hierarchical cluster analysis show that mcDC exhibit a different signature to cDC2. Altogether, we demonstrate that mcDC are a distinct subsets of cDCs with a specific transcriptomic signature.

ORGANISM(S): Mus musculus

PROVIDER: GSE147458 | GEO | 2020/04/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptional analysis of cDC subsets in Irf8+32 -/- and Zeb2 -165(d1+2+3) mice

Project description:To determine if the residual cDC subsets in the Δ1+2+3 and Δ32 mice reflected their normal counterparts, we performed bulk RNA-sequencing analysis of cDC1 and cDC2 from WT, Δ1+2+3 and Δ32 mice. cDC1 from WT and Δ1+2+3 clustered together in principal component analysis (PCA) plot, whereas cDC2 from WT and Δ32 mice cluster together. Further, cDC1 and cDC2 from WT mice show a large number of differentially expressed genes (DEGs), as expected. However, there were few DEGs in cDC1 between WT and Δ1+2+3 mice, or in cDC2 between WT and Δ32 mice, indicating no substantive transcriptional differences between corresponding cDC subsets in WT, Δ32 and Δ1+2+3 mice.

2024-05-29 | GSE268380 | GEO

Cell-autonomous FLT3L shedding via ADAM10 mediates conventional dendritic cell development in mouse spleen

Project description:To characterize the changes that had occurred in splenic pre-cDCs in the absence of ADAM10, we performed RNA sequencing on sorted pre-cDC1 and 2 from the spleens of wild-type and ADAM10ΔDC mice. Unsupervised hierarchical clustering and principal component analysis of all four groups demonstrated that distinct transcriptomic changes had taken place in ADAM10ΔDC pre-cDC2, while minimal changes were observed for pre-cDC1

2019-11-12 | GSE131264 | GEO

Single Cell RNA-Seq Analysis Reveals Fate Decision of Human Pre-cDC Determined by Transcription Factor Competition

Project description:Classic dendritic cells (cDCs) play a central role in the immune system and consist of two major subsets: CD141+ cDC (cDC1) and CD1c+ cDC (cDC2). The pre-cDCs is the immediate precursors to both cDC subsets. Previous studies showed that there were two pre-committed pre-cDC subpopulations. However, the key molecular drivers of pre-commitment in human pre-cDCs were not investigated. To address this question, we performed both single cell and bulk RNA sequencing (RNA-seq) of two cDC subsets and pre-cDCs. We inferred a list of sixteen candidate master regulator transcriptional factors (TFs) that can indeed separate pre-cDCs into two sub-populations, with one close to cDC1 and the other close to cDC2. More importantly, these two pre-cDC sub-populations are correlated with ratio of IRF8 to IRF4 expression level more than their individual expression level. Our results suggest the concept that the ratio of antagonistic TFs and their competition determine cDC subset differentiation fate.

2019-07-16 | GSE89322 | GEO

Absence of Batf3 reveals a new dimension of phenotypic cell state plasticity within conventional dendritic cells

Project description:Conventional dendritic cells (cDCs) are traditionally subdivided into cDC1 and cDC2 lineages. Batf3 is a cDC1-required transcription factor, and we observed that Batf3-/- mice harbor a population of cDC1-like cells co-expressing cDC2-associated surface molecules. Using single cell RNA sequencing with integrated cell surface protein expression (CITE-seq), we found that Batf3-/- mitotic immature cDC1-like cells showed reduced expression of cDC1 features and increased levels of cDC2 features. In wildtype, we also observed a proportion of mature cDC1 cells expressing surface features characteristic to cDC2, and found that overall cDC cell state heterogeneity was mainly driven by developmental stage, proliferation and maturity. We detected population diversity within Sirpa+ cDC2 cells, including a Cd33+ cell state expressing high levels of Sox4 and lineage-mixed features characteristic to cDC1, cDC2, pDCs and monocytes. In conclusion, these data suggest that multiple cDC cell states can co-express lineage-overlapping features, revealing a level of previously unappreciated cDC plasticity.

2021-02-24 | GSE149544 | GEO

scRNAseq of sorted splenic MHCII+ cells from 9 day-old female Clec9a-Cre/Cre Rosa-tdTomato/tdTomato mice after exclusion of CD19+ B cells and autofluorescence+F4/80hi macrophages

Project description:We use scRNA sequencing of MHCII+ cells in the neonatal spleen to elucidate the heterogeneity in young cDC populations and their potential ontogenetic relationship with MHCII-expressiong ILCs. Additionally, we aim to uncover the transcriptomic differences of TOM+ cDC2 and TOM- DC2 in the single cell level. Our data reveal that the neonatal spleen consists of the same cDC1 and cDC2 subsets that comprise the adult cDC compartment. Additionallu, ILCs do not seem to relate otogenetically with TOM- DC2.In the cDC2 clusters, TOM+/- cells are evenly distributed indicative of their transciptomic resemblance. A unique and distinct cluster of TOM- DC2 is observed.

2020-11-06 | GSE151592 | GEO

Irf8 deficiency induces functional, transcriptional and epigenetic reprogramming of cDC1 into the cDC2 lineage

Project description:Conventional dendritic cells (cDC) consist of two functionally and phenotypically distinct subsets, cDC1 and cDC2, whose development is dependent on distinct sets of transcription factors. Interferon regulatory factor 8 (IRF8) is required at multiple stages of cDC1 development, but its role in mature cDC1 remains unclear. Here we used XCR1-cre to delete Irf8 in committed cDC1 and demonstrate that Irf8 is required for maintaining the identify of cDC1 but not their survival. In the absence of Irf8, committed cDC1 (“ex-cDC1”) acquired the transcriptional, functional and chromatin accessibility properties of cDC2. This conversion was independent on Irf4 and was associated with decreased accessibility in putative IRF8, Batf3 and composite AP-1-IRF (AICE) binding elements, together with increased accessibility of cDC2 associated transcription factor binding elements. Thus, IRF8 expression by committed cDC1 is required for preventing their conversion into cDC2.

2022-06-21 | GSE168477 | GEO

Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells

Project description:Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA "barcoding" and single-cell transcriptome and phenotype analysis (CITE-Seq). Inducible tracing of Cx3cr1+ hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1+ progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-Seq analyses of differentiating HSCs and Cx3cr1+ progenitors identified progressive stages of pDC development including Cx3cr1+ Ly-6D+ propDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs, and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s

2022-02-16 | GSE193733 | GEO

A subset of type I conventional dendritic cells control cutaneous bacterial infections through VEGFa-mediated recruitment of neutrophils [single-cell RNA-seq]

Project description:Skin conventional dendritic cells (cDC) exist as two distinct subsets, cDC1 and cDC2, which maintain the balance of immunity to pathogens and tolerance to self and microbiota. Here we examined the roles of dermal cDC1 and cDC2 during bacterial infection, notably Propionibacterium acnes (P. acnes). cDC1, but not cDC2, regulated the magnitude of the immune response to P. acnes in the murine dermis by controlling neutrophil recruitment to the inflamed site and survival and function therein. Single-cell mRNA sequencing revealed that this regulation relied on secretion of the cytokine VEGFα by a minor subset of activated EpCAM+CD59+Ly6D+ cDC1. Neutrophil recruitment by dermal cDC1 was also observed during S. aureus, BCG or E. coli infection, as well as in a model of bacterial insult in human skin. Thus, skin cDC1 are essential regulators of the innate response in cutaneous immunity, with roles beyond classical antigen presentation.

2019-04-13 | GSE129740 | GEO

A subset of type I conventional dendritic cells control cutaneous bacterial infections through VEGFa-mediated recruitment of neutrophils [bulk RNA-seq]

2019-04-13 | GSE129738 | GEO

A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation

Project description:Dendritic cells (DC) are professional antigen presenting cells that develop from multipotent progenitors (MPP) and DC committed common DC progenitors (CDP) and further differentiate into different subsets: classical DC type 1 and 2 (cDC1 and cDC2, respectively) and plasmacytoid DC (pDC). In this study MPP, CDP, cDC1, cDC2 and pDC were obtained in a two-step in vitro culture system according to Felker et al., J. Immunol. 185, 5326-5335, 2010. Briefly, mouse bone marrow cells were first amplified with a specific cytokine cocktail and then induced to differentiate into DC with Flt3 ligand. MPP, CDP, cDC1, cDC2 and pDC were obtained by FACS sorting as follows: MPP: Gr1- CD117hi CD135low/-; CDP: Gr1- CD117int CD135+ CD115+; cDC1: CD11c+ CD11blow/- XCR1+; cDC2: CD11c+ CD11b+ XCR1- and pDC: CD11c+ CD11b- B220+. FACS sorted cells were then subjected to Omni-ATAC-seq, nuclear-titrated (NuTi) Capture-C targeting Irf8 promoter, and RNA-seq analysis. ATAC-seq data of cDC1 and pDC are published (Li et al., Genome Biol. 20, 45, 2019; GSE118221). ATAC-seq data of MPP, CDP and cDC2, NuTi Capture-C and RNA-seq data of MPP, CDP, cDC1, cDC2 and pDC are published here. CD11c+ CD11b+ B220- cDC and CD11c+ CD11b- B220+ pDC were obtained by FACS sorting and subjected to ChIP-seq analysis of IRF8 and are published here.

2023-03-01 | GSE198651 | GEO

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