The two compounds are freely soluble in cell media to a concentration of 500 μM, if they are first dissolved in DMSO. Thus, when determining the GARD input concentration, 500 μM will be Rapamycin datasheet the high end of the titration range. Cell stimulations were performed as described, and harvested cells were stained with PI (Fig. 2A). The relative viability of cells stimulated with 2-nitro-1,4-phenylendiamine decreases with increasing stimuli concentration. The Rv90 value for this compound is identified at a concentration of 300 μM. In contrast, methyl salicylate does not have any cytotoxic effect on MUTZ-3, as the relative viability

remains unchanged with increasing stimuli concentration. Thus, the GARD input concentrations for 2-nitro-1,4-phenylendiamine and methyl salicylate are 300 and 500 μM, respectively. Once the GARD input concentration for all samples to be assayed are established, cell stimulations for 24 h are repeated. Cells are harvested, RNA is isolated, cDNA is prepared and arrays are hybridized as described. Both stimulations are performed in triplicate, independent experiments. Thereafter, the array data from the triplicate stimulations are normalized,

together with available training data, with the RMA algorithm, In this case, the training data refer to the remaining 36 stimulations and vehicle controls used for the establishment of the GARD Prediction Signature (Johansson et al., 2011), a total Alectinib of 131 arrays. At this point, the training data is used for training an SVM model. The model is then used to classify the test data, i.e. 2-nitro-1,4-phenylindiamine and methyl salicylate, as either sensitizer or non-sensitizer (Fig. 2B). The

obtained decision values for this experiment BCKDHB are presented in Table 1. The reproducibility of GARD was determined by assessing the correlation between the triplicate samples of each of the 38 reference chemicals used for assay development. RNA from these triplicate samples were collected at different days and on different batches of cells. Thus, biological variations in terms of cell cycle and growth rate are integrated in the assessment of reproducibility, as well as technical variation during RNA isolation, array hybridization and variation between array batches. The variation in raw signal was assessed by studying Pearson’s correlation coefficient (Table 2). The correlation coefficient is calculated by comparing data for the 200 genes in the GARD Prediction Signature, or for data derived from the complete array. For the GARD Prediction Signature, the correlation coefficient is 0.99 or above in 86% of all comparisons made. The lowest correlation between replicates is observed for penicillin G and p-phenylendiamine, with a coefficient of 0.97. When comparing replicates based on the full array, only Penicillin G has a coefficient below 0.99. Thus, the data is highly reproducible, with stable expression levels of the measured transcripts in technical and biological replicates.