Extended Data Fig. 5. MERVL-KD only dysregulates a few types of transposable element.
(a) Dot plots showing RPKM values for MERVL-int and MT2_Mm in scrambled control and MERVL-KD embryos at two-cell, four-cell, and eight-cell stages. Central bars represent medians, the top and bottom lines encompass 50% of the data points. (b) MA plots show differentially expressed (DE) repetitive elements (annotated in RepeatMasker) between scrambled control and MERVL-KD embryos. DE repeats were defined as those with a |FoldChange| ≥ 2 and Padj < 0.05 (binomial test with Benjamini–Hochberg correction) and shown in red circles. MERVL-int and MT2_Mm were included in downregulated repeats. (c) Violin plots indicate CPM values for chimeric fusion transcripts in scrambled control and MERVL-KD two-cell stage embryos. Each plot encompasses box plot; central bars represent medians, box edges indicate 50% of data points, and the whiskers show 90% of data points. N.S., not significant, two-tailed unpaired t-tests. Data for panels in a-c are available as source data.