Figure 3.

Comparative analyses of the transcriptomic profiles of the Brain-Chip, adult cortex tissue, and transwell culture

(A) Principal component analysis (PCA) of RNAseq data from the brain channel of the Brain-Chip and the transwell brain cells culture on culture days 5 and 7 (n = 4 independent Brain-Chips (donor 1) per condition). The first two PCs explain the 47.47% of the total variance.

(B) DGE analysis identified up (cyan)- and down (magenta)regulated genes (dots) in the Brain-Chip as compared to transwells on culture day 7.

(C and D) Biological processes in Brain-Chip and transwells, as identified by Gene Ontology (GO) enrichment analysis based on the DE genes.

(E) Boxplots summarizing the distributions of the corresponding pairwise TSD distances. In each pair, one sample belongs to the reference tissue (Human Brain-Cortex) and the other either to the reference tissue or to one of our culture models, i.e., Brain-Chip or transwell, from culture days 5 and 7. The Brain-Chip and transwell cultures were run in parallel. n = 4 independent Brain-Chips (donor 1); data are represented as mean ± SEM NS: Not Significant, ∗∗p < 0.01, ∗∗∗p < 0.001; statistical analysis with two-sample t-test using a null hypothesis that the data from human tissue and the data from chips or transwells comes from independent random samples from normal distributions with equal means and equal but unknown variances. On each box the red line indicates the median and the bottom and top edges correspond to the 25^th and 75^th percentiles, respectively. The whiskers extend to the most extreme but not considered outliers values.