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Transcriptomic analysis of thymic epithelial cells and extra thymic epithelial cells

ABSTRACT: Transcriptomic analysis of thymic epithelial cells and extra thymic epithelial cells

PROVIDER: PRJNA604706 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11013500.fastq.gz	Fastqsanger.gz
	SRR11013501.fastq.gz	Fastqsanger.gz
	SRR11013502.fastq.gz	Fastqsanger.gz
	SRR11013503.fastq.gz	Fastqsanger.gz
	SRR11013504.fastq.gz	Fastqsanger.gz

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Single cell transcriptomic analysis of thymic epithelial cells

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Transcriptomic analysis of thymic epithelial cells and extra thymic epithelial cells

Project description:Regulation of MHC I expression has been studied almost exclusively in hematolymphoid cells. We report that thymic epithelial cells (TECs), particularly in the medulla (mTECs), constitutively express up to 100-fold more cell surface MHC I proteins than epithelial cells (ECs) from the skin, colon and lung. Differential abundance of cell surface MHC I in primary ECs is regulated via transcription of MHC I and of genes implicated in the generation of MHC I-binding peptides. Superior MHC I expression in TECs is unaffected by deletion of Ifnar1 or Ifngr1, but is lessened by deletion of Aire, Ifnlr1, Stat1 or Nlrc5, and is driven mainly by type III IFN produced by mTECs. Ifnlr1−/− mice show impaired negative selection of CD8 thymocytes, and at 9 months of age, present autoimmune manifestations. Our study shows unanticipated variation in MHC I expression by ECs from various sites and provides compelling evidence that superior expression of MHC I in TECs is crucial for proper thymocyte education.

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Single cell transcriptomic analysis of thymic epithelial cells

Project description:Single cell transcriptomic analysis of wildtype and AireKO thymic epithelial cells

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Project description:Complementary transcriptomic analysis of human medullary thymic epithelial cells

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Project description:Transcriptome comparison of human Extra-thymic AIRE expressing cells to medullary thymic epithelial cells and conventional antigen presenting dendritic cells.

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RNA-Seq of cultivated (i) bulk human thymic epithelial cells (hTECs) (ii) cortical hTECs (iii) medullary hTECs (iv) human thymic interstitial cells (hTICs)

Project description:Transcriptomic profiling of cultivated human thymic epithelial cells and thymic interstitial cells.

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Expression data from meduallar thymic epithelial cells and thymic or splenic B cells

Project description:Aire is a transcriptional regulator that induces promiscuous expression of thousands of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive. We used Affymetrix microarrays to analyze the gene expression patterns of Aire expressing cells (mature mTECs and Thymic B cells) and compared them to control counterparts, namely immature mTECs, cortical Thymic epithelial cells and splenic B cells of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive. We used Affymetrix microarrays to analyze the gene expression patterns of Aire expressing cells (mature mTECs and Thymic B cells) and compared them to control counterparts, namely immature mTECs, cortical Thymic epithelial cells and splenic B cells.

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Project description:Analysis of thymic epithelial cells lacking Meis1 gene using K14-CreERT2 Meis1fl/fl mice. Meis1 is a TALE class homeodomain transcription factor that critically regulates numerous embryonic developmental processes. Results provide insight into the role of Meis1 in the maintenance of postnatal thymic epithelial cells. Meis1-regulated gene expression in CD45- EpCAM+ mouse thymic epithelial cells was measured at 4 days after the induction of Meis1 deletion. Two independent experiments (pools of 6 mice; 2 pools per genotype) were performed.

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microRNA expression in thymic epithelial cells

Project description:Thymic epithelial cells (TECs) support T cell development in the thymus. Cortical thymic epithelial cells (cTECs) facilitate positive selection of developing thymocytes whereas medullary thymic epithelial cells (mTECs) facilitate the deletion of self-reactive thymocytes in order to prevent autoimmunity. The mTEC compartment is highly dynamic with continuous maturation and turnover, but the genetic regulation of these processes remains poorly understood. MicroRNAs (miRNAs) are important regulators of TEC genetic programs since miRNA-deficient TECs are severely defective. However, the individual miRNAs important for TEC maintenance and function and their mechanisms of action remain unknown. Here, we demonstrate that miR-205 is highly and preferentially expressed in mTECs during both thymic ontogeny and in the postnatal thymus. This distinct expression is suggestive of functional importance for TEC biology. Genetic ablation of miR-205 in TECs, however, neither revealed a role for miR-205 in TEC function during homeostatic conditions nor during recovery from thymic stress conditions. Thus, despite its distinct expression, miR-205 on its own is largely dispensable for mTEC biology. In order to identify miRNAs differentially expressed in mTECs, we purified cortical thymic epithelial cells (cTECs), mTECs and CD45+ cells as three distinct populations and prepared RNA for microarray analysis. Thymic subsets were FACS-purified from 4-week old NOD wildtype mice. Thymi from 10-12 female mice were pooled together for stromal cell isolation for a total of 3 CD45+, 2 cTEC and 3 mTEC biologic replicates.

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Qualitative changes in cortical thymic epithelial cells drive postpartum thymic regeneration.

Project description:Qualitative changes in cortical thymic epithelial cells drive postpartum thymic regeneration.

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