Fig. 5

Plate-based format of 3’Pool-seq applied to differentiate gene expression responses between troglitazone and pioglitazone treatments. a Layout of plate-based 3’Pool-seq using row pooling scheme. Principal component analysis using ERCC spike-ins is used to assess row effect b and column effect c. 95% confidence eclipses are shown for each row or column groups. Row effect is observable as indicated by the strong correlation of row groups with PC1 (R² = 0.53), while column effect is not observed (correlation of column groups with PC1 R² = 0.11). d Differentially expressed genes identified at different doses and time points for the two PPARγ agonists. Row I.D.s were used in the differential expression analysis to correct for row pooling effect. e DE genes identified upon 16 h 25 μM troglitazone treatment showed little differential changes in 16 h 25 μM pioglitazone treatment