Fig. 4
SLAM-seq correlates well with 4tU-seq and identifies extensive differential expression following Bdf1/2 depletion. A Scatterplot comparing log2 fold change in transcription following Bdf1/2 depletion determined using SLAM-seq or 4tU-seq across 4882 transcripts. T > C read counts derived from SLAM-seq were normalized using size factors calculated on total read counts from exogenous whole cell spike-in. Mean values for three biological replicates are plotted. Read counts derived from previously published 4tU-seq data were normalized using size factors calculated on total read counts from exogenous whole cell spike-in. Spearman’s correlation coefficient (rs) is shown. B Volcano plot comparing − log10 false discovery rate (FDR) adjusted p-value and log2 fold change in transcription following Bdf1/2 depletion across 5311 transcripts. T > C read counts were normalized using size factors calculated on total read counts from exogenous whole cell spike-in. Mean values for three biological replicates are plotted. Differentially expressed genes are defined using an FDR adjusted p-value ≤ 0.05 and log2 fold change ≥|1| as cutoffs. Numbers of differentially expressed genes are shown in respective regions of the plot. C Scatterplot comparing log2 fold change in transcription following Bdf1/2 depletion determined using SLAM-seq or 4tU-seq across 4882 transcripts. T > C read counts derived from SLAM-seq were normalized size factors calculated on total read counts. Mean values for three biological replicates are plotted. Read counts derived from previously published 4tU-seq data were normalized using size factors calculated on total read counts from exogenous whole cell spike-in. Spearman’s correlation coefficient (rs) is shown. D Volcano plot comparing − log10 false discovery rate (FDR) adjusted p-value and log2 fold change in transcription following Bdf1/2 depletion across 5311 transcripts. T > C read counts were normalized using size factors calculated on total read counts. Mean values for three biological replicates are plotted. Differentially expressed genes are defined using an FDR adjusted p-value ≤ 0.05 and log2 fold change ≥|1| as cutoffs. Numbers of differentially expressed genes are shown in respective regions of the plot