GEO DataSets

(Submitter supplied) 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). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

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(Submitter supplied) 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). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

10 Samples

Download data: CSV

(Submitter supplied) Medullary thymic epithelial cells (mTECs) play a critical role in central immune tolerance by mediating negative selection of autoreactive T cells through the collective expression of the peripheral self-antigen compartment, including tissue-specific antigens (TSAs). Recent work has shown that gene expression patterns within the mTEC compartment are remarkably heterogenous and include multiple differentiated cell states. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

7 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL24973 GPL21103

30 Samples

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(Submitter supplied) Thymic epithelial cells (TEC) guide selection of a T-cell repertoire that is reactive to pathogens but tolerant to self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire by TEC, the extent to which these cells reproduce peripheral isoform structures is unknown. We performed a transcriptomic investigation of transcript structures and splicing factor expression in medullary TEC and 21 peripheral tissues. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL21103

8 Samples

Download data: CSV, GTF

(Submitter supplied) Thymic epithelial cells (TEC) guide selection of a T-cell repertoire that is reactive to pathogens but tolerant to self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire by TEC, the extent to which these cells reproduce peripheral isoform structures is unknown. We performed a transcriptomic investigation of transcript structures and splicing factor expression in medullary TEC and 21 peripheral tissues. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24973

6 Samples

Download data: TXT

(Submitter supplied) Thymic epithelial cells (TEC) guide selection of a T-cell repertoire that is reactive to pathogens but tolerant to self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire by TEC, the extent to which these cells reproduce peripheral isoform structures is unknown. We performed a transcriptomic investigation of transcript structures and splicing factor expression in medullary TEC and 21 peripheral tissues. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: TXT

(Submitter supplied) mTEC/Tcell crosstalk drives epigenetic programs conditioning immunological tolerance

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BED, WIG

(Submitter supplied) mTEC/Tcell crosstalk drives transcriptional and epigenetic programs conditioning immunological tolerance

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: XLSX

(Submitter supplied) Analysis of gene co-expression patterns in TRA-specific medullary thymic epithelial cell (mTEC) subsets. The whole genome gene signatures of purified mTEC subsets respectively positive for the TRAs Gp2, Pdpn, Cea1, Gad1, Ins2, Tspan8 were compared to their corresponding TRA-negative mTEC subset control. Results provide the enriched and depleted gene expressions in the different subsets.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17543

35 Samples

Download data: IDAT, TXT

(Submitter supplied) Endogenous retroelements (ERE) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. Despite evidence that some EREs can be expressed at the RNA and protein levels in specific contexts, a systems-level evaluation of their expression in human tissues is lacking. We report that all human tissues express EREs but the breadth and magnitude of ERE expression are very heterogeneous from one tissue to another. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: TXT

(Submitter supplied) Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. We are using a proteogenomic approach, combining RNA-Sequencing and mass spectrometry, to discover TSAs. We performed RNA-Sequencing on human medullary thymic epithelial cells (mTECs) to use them as a "normal control" because they express most known genes and orchestrate T cell selection to induce central tolerance to MHC peptides coded by their vast transcriptome.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: TXT

(Submitter supplied) Promiscuous gene expression (pGE) of numerous self-antigens in thymic epithelial cells (TEC) enables the elimination of self-reactive T cells. The autoimmune regulator (Aire) is the only known molecular determinant driving pGE in the thymus but the existence of Aire-independent mechanisms has been inferred. Here, we analyzed the poly(A)+ transcriptome of TEC populations by RNA-sequencing (RNA-seq) in order to reveal differential features of Aire-induced vs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to evaluate the effect of Autoimmune regulator (Aire) gene disruption in a murine medullary thymic epithelial cells (mTEC 3.10 cell line) on the transcriptome of these cells during its adhesion with thymocytes. The mTEC-thymocyte adhesion is a crucial step for the negative selection of autoreactive thymocytes and prevention of autoimmune diseases. To generate Aire mutant cell clones, a total of 5x10^5 mTEC 3.10 cells were electro-transfected (Lonza Nucleofector) with CRISPR-Cas9 plasmid targeting the Aire Exon 3 (plasmid "all in one" encoding Aire Exon 3 gRNA + Cas9 + GFP, from Sigma-Aldrich). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17543

8 Samples

Download data: IDAT, TXT

(Submitter supplied) Different human mTEC subsets (MUC1, CEACAM5 and SGLT1) were purified by sequential enzymatic digestion (collagenase/dispase, trypsin) followed by enrichment using magnetic beads (CD45 beads, Miltenyi Biotech) and FACS sorting. Cells of the surface phenotype CD45-, CDR2-, EpCAM+ were further subdivided into MUC1+/MUC1-, CEACAM5+/CEACAM5- and SGLT1+/SGLT1- fractions. RNA was isolated using μMACS™ SuperAmp™ protocol (Miltenyi Biotec) and hybridized to Illumina Whole-Genome Expression Beadchips. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL13376 GPL6884

26 Samples

Download data: TXT

(Submitter supplied) Background: In order to become functionally competent but harmless mediators of the immune system, T cells undergo a strict educational program in the thymus, where they learn to discriminate between self and non-self. This educational program is, to a large extent, mediated by medullary thymic epithelial cells (mTECs) that have a unique capacity to express, and subsequently present a large fraction of body antigens. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

1 Sample

Download data: TXT

(Submitter supplied) This study set out to assay the (polyA+) transcriptomes of single mature (MHCII high) mouse medullary thymic epithelial cells (mTEC).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

174 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL11002

194 Samples

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