Gene expression data in MSCs 3 weeks post treatment. qRT-PCR results for human mesenchymal stem cells (MSCs) (n = 3) pelleted in 3D culture and treated with conditioned media from four groups: B = Basal, C = Chondrogenic, NCA = notochordal NP cells in alginate; NCT = notochordal NP cells in tissue for 21 days. Fold change in mRNA levels were calculated with the ΔΔCT method relative to three housekeeping genes and undifferentiated (Day 0) MSCs from the same patient. * indicates significantly different from Day 0 and bar indicates significantly different from Basal, P < 0.05; Error bars are expressed as SEMs. 1A: Phenotypic marker/Matrix-associated protein genes. The most prominent results were the significant increase in Sox9 and Col2A1 for NCT media compared to basal and the significant decrease in Col 1A1 and Col3A1 for NCA media; B: Catabolic/anti-catabolic genes. All media conditions had high expression levels for catabolic genes. Very low levels of mRNA for catabolic proteins resulted in very high relative expression levels relative to Day 0 controls. Most relevant comparisons, therefore, are with other groups; C: Growth factor genes. A general up-regulation in expression was observed in particular for NCT, with the exception of CTGF with all media groups; D: Inflammatory/pain genes. Up-regulation of pro-inflammtory cytokines was noted for NCA and NCT however significant down-regulation of NGF was observed with NCT.