Fig. 2

AID2 improved gene expression analysis by SLAM-seq. a Schematic diagram illustrating the SLAM-seq experiment. b Unsupervised data dimensionality reduction by PCA of the top 3000 most variably expressed nascent transcripts (summarized at the gene level) as determined by median absolute deviation. SLAM-seq quantified nascent gene expression from CTCF^AID1 and CTCF.^AID2 cells that underwent AID1 or AID2 auxin treatment conditions over a 24-h time course. Time 0 samples were untreated. RNA was collected following 0, 2, 6, 12, and 24 h of AID1 treatment and after 0, 2, 4, 6, 12, and 24 h of AID2 treatment. Samples for each time point were performed in duplicate. c Venn diagrams highlight the comparison of T > C converted reads (termed nascent and colored red) and all or total reads (termed steady-state and colored blue) of DE genes identified in each corresponding AID1 or AID2 auxin depletion SLAM-seq time-course experiment. DE genes determined in both nascent and steady states are colored purple. Genes passing thresholds of p value ≤ 0.05 and |log₂(FC)|≥ 1 were determined to be differentially expressed. T0 = no AID treatment; T2 = 2-h AID treatment; T4 = 4-h AID treatment; T6 = 6-h AID treatment; T12 = 12-h AID treatment; T24 = 24-h AID treatment. d Gene set enrichment analysis of nascent transcripts summarized at the gene level corresponding to AID1 or AID2 auxin depletion SLAM-seq time-course experiments. Up-regulation and down-regulation by normalized enrichment score (NES) of hallmark gene sets compared to T0 are denoted in red and blue, respectively. Circle size indicates the false discovery rate (FDR)