Cell state · L2
IPSC.axial_identity_primed
8,694 cells in the full atlas (not the displayed sample).
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Marker genes
CTXN1, DNM1P35, FAM200A, FOXB1, HNRNPM, HOXA-AS2, HOXA3, HOXA9, HOXB8, RBM42, SMARCA5, SOX2, THAP2
Annotation genes
HOXA3, HOXA9, HOXB8, SOX2
Annotation rationales
Posterior HOX transcription factors HOXA3/HOXA9/HOXB8 are concomitantly expressed with core pluripotency factor SOX2, indicating that these iPSCs have begun axial patterning while retaining self-renewal circuitry. The co-occurrence of multiple posterior HOX paralogs suggests chromatin opening across the A/B clusters (supported by chromatin remodelers in the gene list), consistent with in vitro “patterning-primed” pluripotency that often precedes directed differentiation to posterior neuroectoderm or mesoderm. Mentioning HOXA3, HOXA9, HOXB8, SOX2 captures the intended axial/identity priming while preserving pluripotent competency.
Functional implications
Functions as a posterior identity–poised pluripotent pool: readily converts into posterior neural (hindbrain/spinal) or paraxial mesoderm fates upon WNT/FGF/RA cues while maintaining self-renewal until patterning signals are provided. Enables synchronized, efficient posterior lineage induction in differentiation protocols.
Marker and functional descriptions are atlas annotations. Explore gene expression, trait associations and regulatory elements in the interactive browsers; see the browser guide.