Fig. 4: Transcriptomic analysis of naïve hPSCs cultured under static, static suspension, and stirred suspension culture.

a RNA-sequencing analysis of naïve H9 hPSCs cultured under stirred suspension and static culture. b RNA-sequencing analysis of naïve H9 hPSCs cultured under stirred suspension and static suspension culture. The violin plots show the enriched canonical pathways in the stirred suspension compared to static and static suspension cultures (selected as control references) based on ingenuity pathway analysis (IPA). The IPA z-score algorithm was used to identify enriched canonical pathways that are more active (positive z-score) or less active (negative z-score) according to the IPA database and observed gene expression in our RNA-seq dataset. Activated = genes expected to be upregulated (positive log2FC) if the pathway is activated according to IPA canonical pathway database. Inactivated = genes expected to be downregulated (negative log2FC) if the pathway is activated according to IPA canonical pathway database. No-expect = no direction of change expectation is available in the IPA canonical pathway database. Filter criteria for pathway enrichment significance was expected direction of change Z-score ≥2 or ≤−2, and –log10 (Benjamini–Hochberg multiple testing corrected p value of differential expression) ≥2. All the suspension cultures underwent fed-batch condition (60% media change, 48-h post-inoculation). Aggregates of day 4 post-cultures were collected for the analysis. The data presented are generated from bioreactor inoculation density of 50,000 cells/mL. The data are representative of three replicates.