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SRX15018769: GSM6070088: medullary thymic epithelial cells, immature, donor 212 [pt212_lo_5'Cap]; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 10.2M spots, 896.4M bases, 366.1Mb downloads

External Id: GSM6070088_r1
Submitted by: Cold Spring Harbor Laboratory
Study: Transcriptome diversity in human medullary thymic epithelial cells - 5'Cap sequencing
show Abstracthide Abstract
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. 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
Sample: medullary thymic epithelial cells, immature, donor 212 [pt212_lo_5'Cap]
SAMN27918940 • SRS12767548 • All experiments • All runs
Organism: Homo sapiens
Name: GSM6070088
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: CAGE
Layout: PAIRED
Construction protocol: mTECs were sorted as CD45-, CDR2-, EPCAM+ cells and MHCII (HLA-DR) was used to separate immature mTEClo and mature mTEChi cell populations RNA from sorted mTEChi and mTEClo populations was extracted using the High Pure RNA Isolation Kit (Roche) The libraries were prepared manually as described in Pelechano (2014) Nature Protocols ; yielding libraries only containing molecules derived from 5'Cap RNA.
Runs: 1 run, 10.2M spots, 896.4M bases, 366.1Mb
Run# of Spots# of BasesSizePublished


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