Extended Data Fig. 3: Transcriptomic profiling of GV oocytes with indicated genotypes.
From: Auto-suppression of Tet dioxygenases protects the mouse oocyte genome from oxidative demethylation
a, Scatter plot of the differentially expressed genes and Transposon Elements (TEs) in Loop KO oocytes. The TEcount function of TE transcripts (v2.2.1)67 was applied to count TEs and genes. b, Gene ontology analysis of the DEGs in the LCD KO oocytes. A two-tailed test for log2FoldChange was performed for analysis, and the p-values were corrected for multiple testing. c, Clustering of GV oocytes according to the distinct genotypes as shown by principal component analysis on TE transcription. Each dot represents a biological replicate. Ten oocytes were pooled for the preparation of each RNA-seq library. WT, LCD KO, LCD, Dnmt3a DKO, LCD KO HD-Mut, Tet3 KO and Dnmt TKO (Dnmt1f/f, Dnmt3af/f, Dnmt3bf/f; Zp3-cre): n = 6, 7, 2, 5, 2 and 2 replicates respectively. d, Transcriptional profiles of IAPs in RNA-seq analysis (raw counts are normalized by library size). WT, LCD KO: n = 6, 7 replicates respectively. Statistical significance (indicated P value) was analyzed using an unpaired two-tailed Student’s t-test.
