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Series GSE201718 Query DataSets for GSE201718
Status Public on Apr 30, 2022
Title Transcriptome diversity in human medullary thymic epithelial cells - 5'Cap sequencing
Organism Homo sapiens
Experiment type Other
Summary 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 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.
Overall design Genome-wide transcription start site analysis using 5'Cap sequencing data for human mature (MHCII high) and immature (MHCII) medullary thymic epithelial cells
Contributor(s) Meyer HV, Carter JA
Citation(s) 35918316
Submission date Apr 27, 2022
Last update date Aug 16, 2022
Contact name Hannah Verena Meyer
Organization name Cold Spring Harbor Laboratory
Street address 1 Bungtown Road
City Cold Spring Harbor
State/province New York
ZIP/Postal code 11724
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (10)
GSM6070085 medullary thymic epithelial cells, mature, donor 87 [pt87_hi_5'Cap]
GSM6070086 medullary thymic epithelial cells, immature, donor 87 [pt87_lo_5'Cap]
GSM6070087 medullary thymic epithelial cells, mature, donor 212 [pt212_hi_5'Cap]
This SubSeries is part of SuperSeries:
GSE201720 Transcriptome diversity in human medullary thymic epithelial cells
BioProject PRJNA832752

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Supplementary file Size Download File type/resource
GSE201718_fivepseq_abundance_tsr.csv.gz 4.3 Mb (ftp)(http) CSV
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