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ATAC-sequencing and RNA-sequencing of innate lymphoid cells that were sorted from mouse skin

ABSTRACT: ATAC-sequencing and RNA-sequencing of innate lymphoid cells that were sorted from mouse skin

PROVIDER: PRJNA491704 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7871420_1.fastq.gz	Fastqsanger.gz
	SRR7871420_2.fastq.gz	Fastqsanger.gz
	SRR7871430_1.fastq.gz	Fastqsanger.gz
	SRR7871430_2.fastq.gz	Fastqsanger.gz
	SRR7871421_1.fastq.gz	Fastqsanger.gz

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ATAC-sequencing of innate lymphoid cells that were sorted from mouse skin

Project description:Purpose: Regulome analysis of skin innate lymphoid cells Methods: Innate lymphoid cells were sorted from epidermis, dermis and subcutis of adult B6 mice, respectively and subjected to transposition reaction and library preparation. Results: 20,869 accessible regulatory elements were detected Conclusions: This study reveals regulome landscape of skin innate lymphoid cells

2018-09-19 | GSE120126 | GEO

RNA-sequencing of innate lymphoid cells that were sorted from mouse skin

Project description:Purpose: Transcriptomic analysis of skin innate lymphoid cells Methods: Innate lymphoid cells were sorted from epidermis, dermis and subcutis of adult B6 mice, respectively and subjected to RNA isolation and library preparation. Results: 3,078 differentially expressed genes (fold change>2 and p-value<0.05) were detected Conclusions: This study reveals transcriptome landscape of skin innate lymphoid cells

2018-09-19 | GSE120128 | GEO

ATAC-sequencing of innate lymphoid cells that were sorted from mouse skin

Project description:ATAC-sequencing of innate lymphoid cells that were sorted from mouse skin

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Single cell RNA-sequencing of innate lymphoid cells isolated from mouse skin layers

Project description:Purpose: Determine the layer-specific indentities and heterogeneity of innate lymphoid cells in the skin by single cell transcriptomic analysis Methods: Innate lymphoid cells were sorted from epidermis, dermis and subcutis of adult B6 mice and subjected to droplet based single-cell captureing and RNA isolation and library preparation. Results: 3,431, 3,356 and 1,061 innate lymphoid cells from epidermis, dermis, and subcutis were analyzed. Unsupervised clustering of the combined data set performed in Seurat identified 6 distinct ILC clusters. Conclusions: This study reveals skin layer-specific transcriptomic signature of innate lymphoid cells

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RNA-sequencing of innate lymphoid cells that were sorted from mouse skin

Project description:RNA-sequencing of innate lymphoid cells that were sorted from mouse skin

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Distinct Gene Regulatory Pathways for Human Innate Versus Adaptive Lymphoid Cells [ChIP-seq & ATAC-seq]

Project description:Innate lymphoid cells (ILCs) serve as sentinels in mucosal tissues, sensing release of soluble inflammatory mediators, rapidly communicating danger via cytokine secretion, and functioning as guardians of tissue homeostasis. Although ILCs have been studied extensively in model organisms, little is known about these âfirst respondersâ in humans, especially their lineage and functional kinships to cytokine-secreting T helper cell (Th) counterparts. Here, we report gene regulatory circuitries for four human ILCâTh counterparts derived from mucosal environments, revealing that each ILC subset diverges as a distinct lineage from Th and circulating natural killer cells, but shares circuitry devoted to functional polarization with their Th counterparts. Super-enhancers demarcate cohorts of cell identity genes in each lineage, uncovering new modes of regulation for signature cytokines, novel molecules that likely impart important functions to ILCs, and potential mechanisms for autoimmune disease SNP associations within ILCâTh subsets. Molecular profiling of innate lymphoid and T helper cells subsets purified from tonsils and NK cells purified from peripheral blood using Assay for Transposase-Accessible Chromatin (ATAC) and chromatin immunoprecipitation (H3K4me3 and H3K27ac).

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Skin-resident innate lymphoid cells converge on a pathogenic effector state

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Project description:Type 2 inflammation contributes to the pathology of skin diseases such as atopic dermatitis and urticaria. Type 2 innate lymphoid cells are key mediators of skin inflammation by releasing type 2 cytokines in response to certain environmental stimuli. We recently found that Rag1 knockout mice exhibit more pronounced skin inflammation in a mouse model of atopic-dermatitis-like disease, despite lacking adaptive immune cells like T helper 2 cells, implicating a critical role of type 2 innate lymphoid cells in this condition. The goal of this study was to characterize transcriptional differences between WT and Rag KO type 2 innate lymphoid cells to determine if Rag knockout leads to cell-intrinsic alterations in innate lymphoid cell function.

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