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RNA-sequencing of Aire-ILC3 cells from wild-type and Aire-deficient mice

ABSTRACT: RNA-sequencing of Aire-ILC3 cells from wild-type and Aire-deficient mice

PROVIDER: PRJEB27961 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2716250.fastq.gz	Fastqsanger.gz
	ERR2716251.fastq.gz	Fastqsanger.gz
	ERR2716252.fastq.gz	Fastqsanger.gz
	ERR2716253.fastq.gz	Fastqsanger.gz
	ERR2716254.fastq.gz	Fastqsanger.gz

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RNA-sequencing of Aire-ILC3 cells from wild-type and Aire-deficient mice

Project description:Autoimmune regulator (Aire) plays an indispensable role in the induction of central immune tolerance. We identify a novel subset of Rorγt-dependent innate lymphoid cell-type in secondary lymphoid organs, which presents endogenously generated antigens and contributes to peripheral T cell tolerance. In this experiment, transcriptomes of these Aire-ILC3 cells are characterized in wild-type Balb/C and Aire-/- Balb/C mice [Ramsey, C. et al. (2002) Hum Mol Genet 11:397-409] using RNA-seq method. To obtain the cells, peripheral lymph nodes were minced, enzymatically digested, and Aire-ILC3 cells were FACS-sorted as Lin-, MHCII+, CD80+, IL7Ra+ cells.

2019-03-14 | E-MTAB-7088 | biostudies-arrayexpress

Transcription profiling of mouse lymphtoxin beta receptor-deficient thymic medullary epithelial cells vs. wild-type and Aire-deficient vs wild-type littermates

Project description:We compared gene expression profiles of lymphotoxin alpha- and lymphtoxin beta receptor-deficient thymic medullary epithelial cells with their wild-type littermates, as well as with Aire-deficient and wild-type littermates. This was done in order to determine whether there was overlap in the effects of lymphotoxin and aire. Experiment Overall Design: Individual thymi were digested with collagenase, dispase and DNAse, and meduallary epithelial cells with the phenotype CD45-G8.8+Ly51intMHCclasssIIhi were isolated by FACS.

2008-06-16 | E-GEOD-8563 | biostudies-arrayexpress

RNAseq analysis of lacrimal glands isolated from wild type and Aire-/- mice at 5 weeks of age

Project description:We used freshly isolated lacrimal glands isolated from wild type and Aire-/- mice on a Balbc background. Mice were 5 weeks of age, with an n=4 for wild type and n=3 for Aire-deficient.

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Expression data from WT and Aire deficient mTECs

Project description:Aire is an important transcription regulator that mediates a role in central tolerance via promoting the promiscuous expression of tissue-specific antigens in the thymus. Although several mouse models of Aire-deficiency have been described, none has analysed the phenotype induced by a mutation that emulates the common 13bp deletion in human APECED by disrupting the first PHD domain in exon 8. Aire-deficient mice with a corresponding mutation showed some disturbance of the medullary epithelial compartment, but at the phenotypic level their T cell compartment appeared relatively normal in the thymus and periphery. An increase in the number of activated T cells was evident, and autoantibodies against several organs were detected. At the histological level, lymphocytic infiltration of several organs indicated the development of autoimmunity, though symptoms were mild and quality of life for Aire-deficient mice appeared equivalent to wild-type littermates, with the exception of male infertility. Vbeta and CDR3 length analysis suggested that each Aire-deficient mouse developed it own polyclonal autoimmune repertoire. Finally, given the prevalence of candidiasis in APECED patients, we examined the control of infection with Candida albicans in Aire-deficient mice. No increase in disease susceptibility was found for either oral or systematic infection. These observations support the view that additional genetic and/or environmental factors contribute substantially to the overt nature of autoimmunity associated with Aire mutations, even for mutations identical to those found in humans with APECED. Keywords: Gene expression comparison between genotypes In this experiment there are 5 samples altogether which consist of two biological replicates of Aire knock-out mTECs and 3 biological replicates of wild type mTECs.

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RNA-sequencing analysis of innate lymphoid cell progenitors from wild-type and circTmem241-deficient mice

Project description:To explore the role of circular RNA,circTmem241, on ILC3 commitment, we isolated ILCPs from wild-type or circTmem241-deficient mice.

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Expression data from WT and Aire deficient mTECs

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Effect of Aire deficiency on peripheral Tgd17 gene expression

Project description:We examine the transcriptional profile of lung Tgd17 cells from mice that are deficient for Aire compared to wild-type mice.

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Expression data of RANKL-deficient CCR6+ ILC3

Project description:Expression data of RANKL-deficient CCR6+ ILC3

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wild type and aire -/- murine meduallary thymic epithelial cells

Project description:Mice used were B6/129 F2's, 3-5 weeks of age, either wild type or with both copies of the autoimmune regulator gene (aire, GenBank #AF079536) disrupted. Thymi from five of these mice of both sexes were removed and pooled. After collagenase/dispase digestion, density gradient fractionation, and fluorescent antibody staining, cells with the phenotype CD45-, G8.8+, CDR1int and B7.1hi were FACS-sorted and total RNA was made from them. RNA was twice-amplified using a T7 polymerase-based method. Keywords: ordered

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