Aire controls gene expression in the thymic epithelium with ordered stochasticity.
The transcription factor Aire controls immunological tolerance by inducing the ectopic thymic expression of many tissue-specific genes, acting broadly by removing stops on the transcriptional machinery. To better understand Aire's specificity, we performed single-cell RNA-seq and DNA-methylation analysis of Aire-sufficient and Aire-deficient medullary epithelial cells (mTECs). Each of Aire's target genes was induced in only a minority of mTECs, independently of DNA-methylation patterns, as small inter-chromosomal gene clusters activated in concert in a proportion of mTECs. These microclusters differed between individual mice. Thus, our results suggest an organization of the DNA or of the epigenome that results from stochastic determinism but is 'bookmarked' and stable through mTEC divisions, which ensures more effective presentation of self antigens and favors diversity of self-tolerance between individuals.
GSE70798 Samples
Cell Metadata and BAM Files
Dataset MetadataBAM Files | Run Accession Number | Sample Accession Number | Organism | Organ/Tissue | Dev. Stage | Cell Type | Sequencer | Protocol | Assay Type | Library Layout | Ontology Term | Cell Cycle Phase |
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BAM Files | Run Accession Number | Sample Accession Number | Organism | Organ/Tissue | Dev. Stage | Cell Type | Sequencer | Protocol | Assay Type | Library Layout | Ontology Term | Cell Cycle Phase |
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Download BAM file for SRR2098998? |
SRR2098998 | SAMN03857390 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2098999? |
SRR2098999 | SAMN03857391 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099000? |
SRR2099000 | SAMN03857392 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099001? |
SRR2099001 | SAMN03857393 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099002? |
SRR2099002 | SAMN03857394 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099003? |
SRR2099003 | SAMN03857395 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099004? |
SRR2099004 | SAMN03857396 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099005? |
SRR2099005 | SAMN03857397 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099006? |
SRR2099006 | SAMN03857398 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
Download BAM file for SRR2099007? |
SRR2099007 | SAMN03857399 | Mus musculus | Thymus | Adult | Thymic epithelial | ILLUMINA | CEL-Seq | RNA-Seq | Single-End | UBERON:0002370 [thymus] | NULL |
FASTQC Report
Bulk DownloadFASTQC File ID | Cell Accession Number | FASTQC Report Link | No. Sequence Tags |
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SRR2098997_1 | SRR2098997 | Preview | 208594 |
SRR2098998_1 | SRR2098998 | Preview | 164555 |
SRR2098999_1 | SRR2098999 | Preview | 342891 |
SRR2099000_1 | SRR2099000 | Preview | 124309 |
SRR2099001_1 | SRR2099001 | Preview | 82855 |
SRR2099002_1 | SRR2099002 | Preview | 133924 |
SRR2099003_1 | SRR2099003 | Preview | 70181 |
SRR2099004_1 | SRR2099004 | Preview | 69874 |
SRR2099005_1 | SRR2099005 | Preview | 385745 |
SRR2099006_1 | SRR2099006 | Preview | 115022 |
Mouse Cell Data
Data Resources
Organism | Run Metadata Link | Data Repository Link | Pubmed Record Link | Author Provided Files | DAVID Annotation Chart Link | DAVID Annotation Table Link | Gene Body Coverage Matrix Link | PCA Matrix Link | Krona Plot Img Link | Unmapped Reads Link | Expression Correlation |
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