Additional file 3: of Tenascin-C expression contributes to pediatric brainstem glioma tumor phenotype and represents a novel biomarker of disease

Figure S3. Unsupervised hierarchical clustering of cell line gene expression profiles RNA-Seq analysis was performed in triplicate on DIPG (n = 3) and HGG (n = 2) cell lines after TNC cDNA, shRNA, and empty vector control transfection. Differentially expressed genes (Log2Fold Change > 2 or < − 2, adjusted p-value < 0.05, X-axis) were identified between cDNA and shRNA lines. a) Unsupervised analysis of resulting gene expression profiles by cell line (Y-axis) demonstrates clustering by technical replicate, followed by experimental condition. b) Scatterplot depicting differential TNC expression levels across shRNA and cDNA cell lines holds when adjusted for cell culture conditions (with or without serum FBS). c) Explicit modeling for differentially expressed genes both as means and as sums across technical replicates results in minimal change in data sets when adjusted for culture conditions. Together, these data demonstrate that observed transcriptomes and resulting cell functions are driven by induced differences in TNC expression. (TIF 136432 kb)