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Transcriptome comparison between Zbtb46-deficient and -sufficient group 3 innate lymphoid cells

ABSTRACT: Transcriptome comparison between Zbtb46-deficient and -sufficient group 3 innate lymphoid cells

PROVIDER: PRJNA753776 | ENA |

REPOSITORIES: ENA

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Transcriptome comparison between Zbtb46-deficient and -sufficient group 3 innate lymphoid cells

Project description:We unexpectedly identify one unique subset of group 3 innate lymphoid cells (ILC3s) that co-expresses Zbtb46, a transcription factor that specifies conventional dendritic cells (cDCs). Zbtb46 is robustly expressed by CCR6+ lymphoid tissue inducer (LTi)-like ILC3s that are developmentally and phenotypically distinct from cDCs. To determine the function of Zbtb46 in ILC3s, we performed RNA sequencing on CCR6+ ILC3s sorted from the large intestine of Zbtb46 f/f and Rorc Cre Zbtb46 f/f mice at steady state.

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Intestinal fibroblastic reticular cell niches control innate lymphoid cell homeostasis and function - Innate lymphoid cells

Project description:Innate lymphoid cells (ILC) in the small intestine govern immune homeostasis and protect the host against gut pathogens. While distinct cell-intrinsic signals have been identified that determine ILC development and differentiation, it has remained unclear which cell population regulates ILC sustenance. Using unbiased single cell RNA transcriptomic analysis of intestinal fibroblasts, we have identified a specialized Ccl19-expressing fibroblastic reticular cell (FRC) population that underpins solitary intestinal lymphoid tissue (SILT) structures including cryptopatches and isolated lymphoid follicles. Conditional ablation of lymphotoxin-β receptor (LTβR) signalling in SILT FRC impeded the maturation of isolated lymphoid follicles and blocked ILC maintenance through the downregulation of IL-7, consequently resulting in the elevated susceptibility to bacterial infection. Moreover, specific Ltbr ablation in FRC during adulthood revealed that constant LTβR-dependent FRC-ILC interaction is required to maintain SILT structures and ILC populations. Taken together, our study unveils a critical intestinal FRC niche that secures protective gut immunity.

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Intestinal fibroblastic reticular cell niches control innate lymphoid cell homeostasis and function - Innate lymphoid cells

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RNA-seq of mouse common lymphoid progenitors, innate lymphoid cell progenitors and NK cell progenitors

Project description:Natural Killer (NK) cells at different developmental stages (common lymphoid progenitor (CLP), innate lymphoid cell progenitors (ILCP), and refined NK progenitor (NKP)) were collected from Vav1+iCre FOXO1,3flox/flox mice (C57BL/6 background). Total RNA was harvested and sequenced with a strand-specific paired-end RNA-seq protocol.

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Induction of human regulatory innate lymphoid cells from group 2 innate lymphoid cells by retinoic acid

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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

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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

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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