TGIRT RNAseq analysis shows transcription differences in shSETX and SETX knock-out U2OS cell lines. RNA samples from control, SETX shRNA (shSETX), and SETX knock-out (KO) U2OS cells were analyzed by TGIRTseq. Differential gene expression is shown in a volcano plot with q value (y axis) and log fold change (x axis) for shSETX compared to control cells (left panels) and SETX KO compared to control cells (right panels). (A–F) Analysis is shown for protein-coding genes (A and B), non-coding RNAs (C and D), and transposable elements (E and F). Transcripts with >1 log₂ fold change difference between treatment and control groups and P values <0.001 are shown in red. See also Table S3.