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Transcriptome diversity in human medullary thymic epithelial cells

ABSTRACT: Transcriptome diversity in human medullary thymic epithelial cells

PROVIDER: PRJNA832748 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18941352_1.fastq.gz	Fastqsanger.gz
	SRR18941352_2.fastq.gz	Fastqsanger.gz
	SRR18941353_1.fastq.gz	Fastqsanger.gz
	SRR18941353_2.fastq.gz	Fastqsanger.gz
	SRR18941354_1.fastq.gz	Fastqsanger.gz

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Transcriptome diversity in human medullary thymic epithelial cells - RNAseq

Project description:Transcriptome diversity in human medullary thymic epithelial cells - RNAseq

| PRJNA832751 | ENA

Transcriptome diversity in human medullary thymic epithelial cells - RNAseq

Project description:The induction of central T-cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs), enabled by a process known as promiscuous gene expression (pGE). Transcriptome diversity generated during pGE has many contributors, including non-canonical transcription initiation, alternative splicing and expression of endogenous retroelements (EREs). However, their significance and regulation are poorly understood in the healthy human thymus. Here, we mapped the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5'Cap and RNA sequencing. Overall, 96\% of protein coding genes were represented across five human mTEC samples, with mature mTECs showing increased rates of global transcript mis-initiation. Both mTEC populations have increased splicing entropy, which appears to be driven by expression of peripheral splicing factors. Furthermore, EREs enriched in long terminal repeat retrotransposons are up-regulated during mTEC maturation and enriched in genomic proximity to differentially expressed genes. We provide an interactive interface to explore the transcriptome diversity we uncovered at http://transcriptomediversity.cshl.edu/. Our findings represent an important first step towards the generation of a comprehensive map of transcriptome diversity in the healthy human thymus. Ultimately, a complete map of thymic expression diversity will allow for the identification of epitopes that contribute to the pathogenesis of auto-immunity and that drive immune recognition of tumor antigens.

2022-04-30 | GSE201719 | GEO

Transcriptome diversity in human medullary thymic epithelial cells - 5'Cap sequencing

Project description:The induction of central T-cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs), enabled by a process known as promiscuous gene expression (pGE). Transcriptome diversity generated during pGE has many contributors, including non-canonical transcription initiation, alternative splicing and expression of endogenous retroelements (EREs). However, their significance and regulation are poorly understood in the healthy human thymus. Here, we mapped the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5'Cap and RNA sequencing. Overall, 96% of protein coding genes were represented across five human mTEC samples, with mature mTECs showing increased rates of global transcript mis-initiation. Both mTEC populations have increased splicing entropy, which appears to be driven by expression of peripheral splicing factors. Furthermore, EREs enriched in long terminal repeat retrotransposons are up-regulated during mTEC maturation and enriched in genomic proximity to differentially expressed genes. We provide an interactive interface to explore the transcriptome diversity we uncovered at http://transcriptomediversity.cshl.edu/. Our findings represent an important first step towards the generation of a comprehensive map of transcriptome diversity in the healthy human thymus. Ultimately, a complete map of thymic expression diversity will allow for the identification of epitopes that contribute to the pathogenesis of auto-immunity and that drive immune recognition of tumor antigens.

2022-04-30 | GSE201718 | GEO

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Complementary transcriptomic analysis of human medullary thymic epithelial cells

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

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Project description:We have found that Cdx1 can promote ectopic gene expression in thymic epithelial cells. We isolated MHCIIhi CD80hi medullary thymic epithelial cells from Cdx1-/- and Cdx1+/+ and compare gene expression between the two subsets, also in the context of Cdx1-mediated changes in intestinal epithelial cells.

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Lymphtoxin pathway effects on thymic medullary epithelial cells

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. Keywords: genetic modification

2007-10-23 | GSE8563 | GEO

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