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Transcriptome analysis of conventional dendritic cells (cDCs) introduced into the thymic microenvironment of re-aggregated thymic organ cultures (RTOCs)

ABSTRACT: Transcriptome analysis of conventional dendritic cells (cDCs) introduced into the thymic microenvironment of re-aggregated thymic organ cultures (RTOCs)

PROVIDER: PRJNA689792 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13360905.fastq.gz	Fastqsanger.gz
	SRR13360906.fastq.gz	Fastqsanger.gz
	SRR13360907.fastq.gz	Fastqsanger.gz
	SRR13360908.fastq.gz	Fastqsanger.gz
	SRR13360909.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of conventional dendritic cells (cDCs) introduced into the thymic microenvironment of re-aggregated thymic organ cultures (RTOCs)

Project description:cDCs home from the periphery into the thymus. In order to determine the phenotypic and functional changes introduced by the thymic microenvironment to these thymus-homing cDCs, RNA-based next generation sequencing (RNAseq) was performed with splenic (sp-DC) and thymic conventional DCs (t-DCs) re-isolated from RTOCs after two days of culture. Methods: RTOCs were generated from single-cell suspensions of thymi isolated from E14.5 to E16.5 fetuses of Foxp3hCD2 reporter mice (BALB/c background), and sp‑DCs or t‑DCs sorted from 4-8 weeks old female CD45.1xBALB/c mice were introduced. After two days of culture, 1‑2x103 cDCs were re-isolated from RTOCs as CD45.1+Lin-CD11chi by FACS, and total RNA for transcriptional profiling by low-input RNAseq was isolated. Total RNA from sp-DC and t-DCs isolated ex vivo from 4-8 weeks old female CD45.1xBALB/c mice was used as control. RNAseq was performed on an Illumina HiSeq2500 system. Differential gene expression between the four different conditions was computed from the read counts. Results: The number of differentially expressed genes between ex vivo isolated sp-DC and t-DC was drastically reduced comparing sp-DCs and t-DCs re-isolated from RTOCs. This finding implies that the thymic microenvironment within an RTOC modulates the gene expression in sp‑DCs, conferring a transcriptomic profile that more closely resembled the one from t‑DCs. Conclusion: The thymic microenvironment modulates the transcriptome of thymus-homing peripheral cDCs.

2021-03-01 | GSE164280 | GEO

Expression data from mouse conventional dendritic cells (cDCs)

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Extracellular vesicles (EV) from IFNγ-primed cardiosphere-derived cells (CDCs)

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2020-05-15 | PXD016434 | Pride

Transcriptome comparison of human Extra-thymic AIRE expressing cells to medullary thymic epithelial cells and conventional antigen presenting dendritic cells.

Project description:The provenance of eTACs is unknown, and their characterisation in humans is currently absent. Using bulk RNA sequencing we compare the endogenous expression capacity for self-antigens between eTACs, mTECs and cDCs.

2019-01-14 | E-MTAB-7383 | biostudies-arrayexpress

Single-cell RNA-seq reveals heterogeneity within human pre-cDCs

Project description:Here, we use a microfluidics-based approach to prepare single-cell RNA-Seq libraries from 164 primary human conventional dendritic cells (cDCs) as well as cord blood (452) and blood (341) pre-cDCs. We examined heterogeneity between individual cells to document potential subpopulations within human cDCs and pre-cDCs.

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Proteomics analysis of myocardial tissue from ischemia/reperfusion (I/R) pig model treated with cardiosphere-derived cells (CDCs)

Project description:Some studies report better outcomes in cell therapy for myocardial infarction (MI) with repeated administrations. We aimed to elucidate the potential differences in terms protein expression after one or three doses of cardiosphere-derived cells (CDCs) in a porcine MI model. CDCs were isolated from swine cardiac explants, cultured in CGM, and prepared for administration. Pigs surviving a 90-minute balloon occlusion of the mid-LAD were randomly allocated to receive vehicle (CON), one (D1) or three (D3) doses of 30x106 CDCs via the infarct-related coronary artery.

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Project description:In this study we therefore focused on 2 heart-derived progenitor cell populations that have been recently introduced in clinical translation, autologous c-kitpos–selected CPCs and CDCs. For the first time we compared molecular signatures and proliferation and differentiation characteristics of progenitor cells from young donor hearts (c-kitpos yCPC and yCDC) with cells obtained from adult donors with advanced ischemic disease (c-kitpos aCPC and aCDC). Here we report that culture expanded CDCs derived from adult donors have a distinct transcriptional profile with greater cell cycle activity and superior in vitro paracrine growth factor release compared to yCDCs. The molecular signature of aduIt CDCs favours cardiac repair via pro-angiogenic, cytotrophic and immunomodulatory effects while cardiac transdifferentiation potential is modest and comparable in all progenitor cell populations.

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comparison of primary epicardium explant derived CDCs and primary Epicardial cells

Project description:The analysis showed differences of transcriptomes between primary epicardium explant derived CDCs and primary Epicardial cells directly isolated from the heart epicardium.SB-431542 was an effective TGF-b pathway inhibitor that could obviously inhibit the epicardial cells Epithelial-mesenchymal transition. SB-432542 treatment could produce some epithelial clones in the CDCs,which showed epicardiac specific expression profile, compared with the CDCs.

2022-02-18 | GSE189275 | GEO

Nanostring of sorted lung conventional dendritic cells (cDCs) from cell-specific MyD88 KO at 6h after in vivo sensitization with OVA/standard flagellin

Project description:Allergic asthma is a chronic disease of the airways characterized by eosinophilic and neutrophilic inflammation. MYD88, the adaptor molecule for TLR and IL-1 family member signaling, is required for allergic sensitization through the airway in animal models of allergic asthma. We generated conditionally mutant mice separately lacking Myd88 in airway epithelial cells (ECs) or dendritic cells (DCs) to define the contribution of Myd88 expression in each of these cell types. To examine crosstalk from ECs to conventional (c)DCs in vivo, we examined immune-specific transcriptional profiles from lung cDCs sorted following 6h in vivo lung allergic sensitization through the airways from WT MyD88 fx/fx, SPC cre+ MyD88 fx/fx (EC-MYD88 KO), CD11c cre+ MyD88 fx/fx (DC-MYD88 KO), and full MyD88 KO mice. We observed immune-specific transcriptional changes in cDCs that were cell-intrinsic as well as resulting from in vivo crosstalk from ECs. We also observed transcriptional (linked data set) and epigenetic changes in chromatin conformation in cDCs by ATAC-seq (linked data set) as well as changes in immune-specific whole lung RNA, sorted EC RNA, and sorted alveolar macrophage (AM) RNA by Nanostring nCounter Immunology Codeset Analysis (additional linked files).

2018-03-10 | GSE79614 | GEO

Array of sorted lung conventional dendritic cells (cDCs) from cell-specific MyD88 KO at 0h and 6h in vivo sensitization with OVA/standard flagellin

Project description:Allergic asthma is a chronic disease of the airways characterized by eosinophilic and neutrophilic inflammation. MYD88, the adaptor molecule for TLR and IL-1 family member signaling, is required for allergic sensitization through the airway in animal models of allergic asthma. We generated conditionally mutant mice separately lacking Myd88 in airway epithelial cells (ECs) or dendritic cells (DCs) to define the contribution of Myd88 expression in each of these cell types. To examine crosstalk from ECs to conventional (c)DCs in vivo, we examined transcriptional profiles from lung cDCs sorted at baseline or following 6h in vivo lung allergic sensitization through the airways from WT MyD88 fx/fx, SPC cre+ MyD88 fx/fx (EC-MYD88 KO), CD11c cre+ MyD88 fx/fx (DC-MYD88 KO), and full MyD88 KO mice. We observed specific transcriptional changes in cDCs that were cell-intrinsic as well as resulting from in vivo crosstalk from ECs. We also observed epigenetic changes in chromatin conformation in cDCs by ATAC-seq (linked data set) as well as changes in immune-specific whole lung RNA, sorted EC RNA, sorted alveolar macrophage RNA, and sorted cDC by Nanostring nCounter Immunology Codeset Analysis (additional linked files).

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