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RNA-seq profiling of cortical and medullary thymic epithelial cells from wildtype and Kat7 knockout mice

ABSTRACT: RNA-seq profiling of cortical and medullary thymic epithelial cells from wildtype and Kat7 knockout mice

PROVIDER: PRJNA780539 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16951105_1.fastq.gz	Fastqsanger.gz
	SRR16951105_2.fastq.gz	Fastqsanger.gz
	SRR16951106_1.fastq.gz	Fastqsanger.gz
	SRR16951106_2.fastq.gz	Fastqsanger.gz
	SRR16951107_1.fastq.gz	Fastqsanger.gz

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ATAC-seq profiling of medullary thymic epithelial cells from wildtype and Kat7-knockout mice

Project description:Thymic epithelial cells govern thymic T lymphocyte differentiation and selection. Medullary TECs (mTECs) facilitate the negative selection of self-reactive thymocytes and the differentiation of FOXP3+ regulatory T cells. Medullary TECs are also distinctive for their “promiscuous” gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. To probe the mechanism by which KAT7 promotes AIRE function, we performed ATAC-seq to compare chromatin accessibility in MHCII-high medullary thymic epithelial cells from Kat7-knockout and wildtype mice.

2021-12-21 | GSE188868 | GEO

RNA-seq profiling of cortical and medullary thymic epithelial cells from wildtype and Kat7 knockout mice

Project description:Thymic epithelial cells (TECs) govern thymic T lymphocyte differentiation and selection. They can be divided into cortical and medullary TECs based on their anatomical location, function and molecular features. Cortical TECs (cTECs) provide the microenvironment for the commitment of haematopoietic precursors to the T lymphoid lineage and mediate the positive selection of CD4+CD8+ double-positive thymocytes. Medullary TECs (mTECs) facilitate the negative selection of self-reactive thymocytes and the differentiation of FOXP3+ regulatory T (Treg) cells2. Medullary TECs are also distinctive for their "promiscuous" gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. To determine the transcriptional impact of Kat7 loss, we purified mTECs and cTECs from Kat7-knockout and control mice and performed RNA-seq. The mTECs were further divided into MHCII-high and MHCII-low subsets.

2021-12-21 | GSE188870 | GEO

ATAC-seq profiling of medullary thymic epithelial cells from wildtype and Kat7-knockout mice

Project description:ATAC-seq profiling of medullary thymic epithelial cells from wildtype and Kat7-knockout mice

| PRJNA780541 | ENA

RNA-seq and ATAC-seq profiling of thymic epithelial cells from wildtype and Kat7 knockout mice

Project description:The autoimmune regulator, AIRE, induces the transcription of thousands of peripheral tissue genes (PTGs) in thymic epithelial cells (TECs) to mediate immunological tolerance. The chromatin state required for optimal AIRE function in TECs and how this state is induced remains unclear. Using RNA-seq and ATAC-seq, we tested the role of the histone acetyltransferase, KAT7 (also known as HBO1 or MYST2), which is essential for acetylation of histone 3 lysine 14 (H3K14), in TEC differentiation, AIRE-mediated PTG expression and thymic tolerance. We find that KAT7 is required for optimal expansion of medullary TEC and has a major role in the expression of AIRE-dependent PTGs, associated with enhanced chromatin accessibility at these gene loci in TECs. Mice with TEC-specific Kat7 deletion develop organ-specific autoimmunity with features resembling those observed in Aire-deficient mice. These findings highlight critical roles for KAT7-mediated acetylation in promoting a chromatin state at PTG loci that enables AIRE function and the establishment of immunological tolerance.

2021-12-21 | GSE188871 | GEO

RNA-seq profiling of epithelial cells from fetal thymic organ cultures from Kat7 knockout and wildtype mice

Project description:Thymic epithelial cells (TECs) govern thymic T lymphocyte differentiation and selection. Medullary TECs are distinctive for their "promiscuous" gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. This experiment was part of a larger study in which we examined the impact of Kat7 loss on AIRE-mediated PTG expression. Despite the apparently normal differentiation of AIRE+ TECs in Kat7-knockout mice, it was possible that the defect in AIRE-mediated PTG expression was secondary to the developmental loss of this histone acetyltransferase. To address this hypothesis, we employed fetal thymic organ cultures (FTOC) depleted of thymocytes where AIRE+ mTEC and PTG expression was induced by an agonist anti-RANK antibody. We then used two different approaches to acutely block KAT7 function and subsequently sort purified TECs for RNA-seq analysis to assess the impact on AIRE-mediated PTG transcription. AIRE+ mTECs exhibit relatively low turnover in organ culture; therefore, this approach uncouples KAT7 impacts on AIRE function from potential influences on TEC differentiation. Our first approach employed a new small molecule inhibitor of KAT7 function, WM-3835. The second approach was an inducible genetic deletion system. FTOC established with thymi from control (Kat7fl/fl) or RosaCre-ERT2 Kat7fl/fl mice were treated with tamoxifen to activate CRE-mediated deletion of Kat7.

2021-12-21 | GSE188869 | GEO

Expression data from cortical thymic epithelial cells ectopically expressing Aire

Project description:Aire in medullary thymic epithelial cells plays an essential role in the negative selection through expression of broad arrays of tissue-restricted antigens. We asked whether Aire could also activate the expression of tissue-restricted antigens in cortical thymic epithelial cells. We established a semi-knockin strain of NOD-background mice expressing Aire under control of the promoter of β5t, a thymoproteasome expressed exclusively in the cortex. We extracted RNA from cortical thymic epithelial cells ectopically expressing Aire and hybridization was performed on Affymetrix. microarrays.

2015-08-03 | E-GEOD-70326 | biostudies-arrayexpress

Single cell transcriptome of cultured thymic cortical and medullary progenitor and stem cells and skin keratinocyte stem/progenitor cells

Project description:Purpose: The goal of this study is to characterise expanding thymic progenitor and stem cells from whole epithelial as well as cortical, medullary thymus sub-compartments. As reference, we have sequenced skin keratinocyte progenitor and stem cells Methods: Cells have been expanded for 4 passages on mouse feeder layer cells then loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina HiSeq 4000. Conclusions: Our study compared thymic progenitor and stem cells from different origin and dissected in vitro properties of thymic and skin progenitor and stem cells

2023-08-30 | GSE220829 | GEO

Expression data from cortical thymic epithelial cells ectopically expressing Aire

2015-08-03 | GSE70326 | GEO

RNA-seq profiling of thymic epithelial cells from Mcl1 knockout and wildtype mice

Project description:T cell differentiation is governed by interactions with thymic epithelial cells (TECs) and defects in this process undermine immune function and tolerance. To uncover new strategies to restore thymic function and adaptive immunity in immunodeficiency, we sought to determine the molecular mechanisms that control life and death decisions in TEC. We created a mouse model which specifically deleted the pro-survival gene Mcl1 in TEC. We found that while BCL-2 and BCL-XL were dispensable for TEC homeostasis, MCL-1 deficiency impacted on TEC as early as E15.5, resulting in early thymic atrophy and T cell lymphopenia, with near complete loss of thymic tissue by 2 months of age. MCL-1 was not necessary for TEC differentiation but was continually required for the survival of medullary TEC, including autoimmune regulator (AIRE) expressing TECs and the maintenance of overall thymic architecture. To understand the molecular mechanisms in more detail, RNA-seq profiling was undertaken of cortical and medullary thymic epithelial cells (cTECs and mTECs) from wildtype and knockout mice.

2017-09-25 | GSE102227 | GEO

Genome-wide analysis of the TEC-specific Hipk2 gene knockout in mouse medullary thymic epithelial cells (mTECs)

Project description:Analysis of the role of Hipk2 in regulating gene expression in medullary thymic epithelial cells. The whole genome gene signatures of purified mTEC subsets (CD80 low, CD80 high) from TEC-specific Hipk2 knockout mice were compared to mating wildtype control mice (floxed, Cre-). Results provide the up- or down-regulated genes, affected by the Hipk2 gene knockout.

2015-01-05 | GSE63432 | GEO

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