Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development
Fig 5
Dynamic expression patterns of TEs during mouse preimplantation embryo development.
(A) UMI counts of each TE superfamily detected in single cells at each stage. The raw data for this plot is supplied in S5 Data. (B) Number of expressed TE loci per cell at each stage. The raw data for this plot is supplied in S5 Data. (C) Expression level of each TE locus (upper panel) and all TE counts (lower panel) belonging to different classes in each stage, satellite was also included. Each dot represents a cell. Only active loci in each cell were calculated. The raw data for this plot is supplied in S5 Data. (D) Expression heatmap of stage specific TEs (n = 3,894 unique loci). The TEs were ordered by their averaged expression levels within each stage (also see S3 Table). The raw data for this plot is supplied in S5 Data. (E) The top5 subfamilies of ERVL expressed in clusters C1–C3 in Fig 5D. (F) The top5 subfamilies of LINE1 expressed in clusters C1–C3 in Fig 5D. (G) Correlation values between expression levels of representative stage-specific LINE1 and ERVL loci (averaged UMI counts >5) and their adjacent genes (<10 kb distance). Non-adjacent genes are defined as genes over 1 Mb away from the TE loci. The raw data for this plot is supplied in S5 Data. (H) Heatmap showing examples of consistent expressions between specific TE loci and their adjacent genes along developmental stages. The raw data for this plot is supplied in S5 Data. LINE, long interspersed element; TE, transposable element.