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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type CD8a+ Dendritic cells upon pIC stimulation

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type CD8a+ Dendritic cells upon pIC stimulation

PROVIDER: PRJNA608467 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11215252.fastq.gz	Fastqsanger.gz
	SRR11215253.fastq.gz	Fastqsanger.gz
	SRR11215254.fastq.gz	Fastqsanger.gz
	SRR11215255.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type CD8a+ Dendritic cells upon pIC stimulation

Project description:Purpose: The goals of this study to understand gene expression at the transcriptional level in CD8a+ Dendritic cells after TLR3 activation by pIC.

2023-01-01 | GSE145672 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NCoR1 KD CD8a+ Dendritic cells with and without CpG stimulation

Project description:Purpose: The goals of this study to dissect mechanism by which NCoR1 regulate expression of diiferent genes at transcriptional level in CD8a+ Dendritic cells. Methods: mRNA expression of Control(Empty) and knockdown (NCoR1+/−) before and after CpG and pIC activation were generated by deep sequencing, in duplicate, using Illumina NextSeq 500 . The sequence reads that passed quality filters were analyzed at the transcript level with two methods:TopHat followed by Cufflinks. Results: we mapped raw reads to the mouse genome (build mm10) with TopHat. Differential expression study was carried out using Cufflinks v2.2.1 and list were filtered using fold change cut-off of 2 and q value <0.05. Conclusions: We found in our study that NCoR1 knock down dendritic cells (DCs) develop tolerogenic behavior upon activation and these cells have the potential to modulate T helper cell differentiation toward Treg phenotype. Here to understand the mechanism of this process we performed NCoR1 ChIP-seq in wild type DCs before and after CpG ligand activation and transcriptome analysis of NCoR1 KD DCs to identify the direct and indirect target genes. We also predicted PU.1 as the recruting factor for NCoR1 in DCs based on motif enrichment and later on validated that by performing PU.1 ChIP-seq in control and NCoR1 KD DCs.

2019-10-18 | GSE110422 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NCoR1 KD CD8a+ Dendritic cells with and without CpG stimulation

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NCoR1 KD CD8a+ Dendritic cells with and without CpG stimulation

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Sheep dendritic cells CD26+ and CD26- versus total dendritic cells

Project description:Transcriptomic profiling of ovine skin lymph dendritic cell subsets CD26+ and CD26- compared to total enriched lymph dendritic cells. CD26+ and CD26- dendritic cells (DC) from sheep skin lymph were sorted by flow cytometry and were analysed for their transcriptomic profile. We demonstrate that the minor sheep CD26+ skin lymph DC subset shares significant transcriptomic similarities with mouse CD8a+ and human BDCA3+ DC. This allowed the identification of a common set of phenotypic characteristics for CD8a-like DC in the 3 mammalian species, i.e. SIRPlo, CADM1hi, CLEC9Ahi, DEC205hi, XCR1hi. Compared to CD26- DC, the sheep CD26+ DC show (1) potent stimulation of allogeneic naive CD8+ T cells with high selective induction of the Ifn-gamma and Il22 genes; (2) dominant efficacy in activating specific CD8+ T cells against exogenous soluble antigen; (3) selective expression of functional pathways associated to high capacity for antigen cross-presentation. Reference design (total enriched lymph dendritic cells) - Biological replicates: 2 sheep #10081 and #30066

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