Cell state · L2
EPI.thymic_cortical.baseline
660 cells in the full atlas (not the displayed sample).
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Marker genes
ARID5A, ARL5B, BIRC3, CLDN7, EIF5, HLA-E, IL32, IRF8, LITAF, NFKBID, NINJ1, PELI1, SAA1, SAA2, SLC12A7, TAP1, TNFRSF12A, UBD
Annotation genes
CLDN7, HLA-E, IRF8, NFKBID, TAP1
Annotation rationales
Cortical TECs (cTECs) present self peptides and maintain an epithelial barrier amid dense thymocyte traffic; TAP1 and HLA-E reflect active antigen processing and non-classical MHC presentation important for selection checkpoints. CLDN7 secures tight junctions shaping cortical microcompartments. IRF/NF-κB modulators (IRF8/NFKBID/BIRC3/PELI1) tune cytokine responses to avoid tissue damage during positive selection.
Functional implications
Provides a stable, semi-permeable antigen landscape for double-positive thymocytes to test TCR affinity. Maintains epithelial integrity and cytokine homeostasis so selection proceeds efficiently without inflammatory disruption, ensuring a diverse, self-tolerant T-cell repertoire.
Marker and functional descriptions are atlas annotations. Explore gene expression, trait associations and regulatory elements in the interactive browsers; see the browser guide.