A multi-modal profiling workflow of transcriptomics and biomineralization demonstrated on a tooth-on-chip model.

tooth-on-chip platforms recapitulate dental epithelial-mesenchymal (DE-DM) interactions, offering physiologically relevant in vitro models for tooth regeneration. However, broader adoption requires chip-scale analytical methods capable of resolving cell-type-specific transcriptional programs and characterizing mineral formation. Here, we present a multi-modal workflow adapting five established approaches to fibrin hydrogel-based tooth-on-chip constructs. Whole-construct RNA extraction yielded high-integrity RNA suitable for bulk RNA sequencing, enabling pooled transcriptional comparisons between dental epithelium and mesenchyme. Magnetic-activated cell sorting achieved efficient recovery and enrichment from chip-relevant cell inputs, while translating this approach to intact constructs revealed a platform-level incompatibility between fibrin dissolution and downstream sorting. Fixation strategies preserved tissue morphology for spatial transcriptomics but came at the cost of RNA quality, and Raman spectroscopy combined with transmission electron microscopy enabled ultrastructural assessment of calcium phosphate deposition, though confirming mature hydroxyapatite required further validation. Together, this workflow establishes a practical framework for benchmarking analytical readouts in fibrin-based tooth-on-chip and related organ-on-chip co-culture systems. Established whole-construct RNA extraction for bulk transcriptional profiling of DE-DM co-cultures Adapted cell sorting and dissociation strategies for cell-type-specific enrichment, identifying key compatibility constraints Applied spatial transcriptomics preparation and spectroscopic/ultrastructural imaging to characterize tissue architecture and calcium phosphate deposition.