Extended Data Figure 4: Transcriptome analysis of Exosc3-deficient B cells.

a, Genome-wide expression level analysis upstream and downstream of TSS region for expressed protein coding genes. Coding genes with FPKM >1 were determined to be expressed. Analysis was restricted to coding genes that do not have any known genes within a 4 kb upstream boundary. Indicated genotypes are on a ROSA26^CreERt2/+ background. One sex-matched littermate pair was used. Two biological replicates were performed. b, Replicate analysis of genome-wide studies. Plots indicate the expression levels of individual genes in Exosc3^WT/WT and Exosc3^COIN/COIN B cells treated with 4-OHT and stimulated with LPS plus IL-4 from two separate littermate pairs. B cells were purified, cultured and FACS sorted, and RNA was purified and sequenced by RNA-seq all independently between the two experiments. Indicated genotypes are on a ROSA26^CreERt2/+ background. Pearson correlation is indicated. c, The distribution of observed lengths for all gapped xTSS-RNAs in Exosc3-deficient B cells. Data were compiled from two biological replicates. d, Scatter plot indicating weak correlation between expression of downstream coding transcript and upstream gapped xTSS-RNA at divergently transcribed loci in Exosc3-deficient B cells. Pearson correlation is indicated. e–g, Profile of RNA-seq mapped reads at the β-actin locus (e) (Actb; 7.6 kb window), Il2rg locus (f) (5.4 kb window) and Ung locus (g) (12 kb window). Indicated genotypes are on a ROSA26^CreERt2/+ background and B-cell cultures were treated with 4-OHT and stimulated with LPS plus IL-4. Four biological replicates were performed.