Table 1. Summary of gene ontology biological process annotations derived from genes most highly expressed in each condition.

Source|Cartilage	Biological Process	Source|Tendon	Biological Process
Native	Immune system process	Native	Muscle system process
	Immune response		Muscle contraction
	Cell cycle		Immune system process
	Defense response		Skeletal muscle tissue development
			Actin filament-based process
Monolayer (chondrocytes)	Single-organism metabolic process	Monolayer (tenocytes)	Cell-redox homeostasis
	Extracellular matrix organisation		Response to endoplasmic reticulum stress
	Oxidation-reduction process		Single organism metabolic process
	Cardiovascular system development
	Developmental process
Alginate cultures	Single-organism metabolic process	Fibrin cultures	Translation
	Oxidation-reduction process		Metabolic process
	Lipid metabolic process		Response to oxidative stress
	Response to oxidative stress		Apoptotic signalling pathway
	Apoptotic signalling pathway		Collagen catabolic process

All functional terms are significantly enriched at FDR <0.001 and filtered for redundant terms. Native cartilage and tendon were annotated with distinct functional terms, but overlapped for immune-associated biological processes. In contrast, monolayer chondrocytes and tenocytes demonstrated frequent overlap in functional annotations (see Supplementary Data, SD2–SD7). The terms ‘response to oxidative stress’ and ‘apoptotic signalling’ were common to fibrin and alginate cultures.