Extended Data Fig. 2: Isoform analysis.
From: Locus-specific expression of transposable elements in single cells with CELLO-seq
(a) expression of TE derived-isoforms in human iPSCs and mouse 2-cell data stratified by whether a repeat acts as a transcript end site (TES) or as a transcript start site (TSS). Mouse: TES (n = 353), TSS (n = 76). Human: TES (n = 537), TSS (n = 73). (B) number of TE derived-isoforms in hiPSCs and mouse blastomeres with repeat as TES or TSS. (c) Barplot of repeat family underlying repeat derived-isoforms in hiPSCs. (d) Barplot of repeat family underlying repeat derived-isoforms in mouse blastomeres. (e) frequency plot of number of repeats (x-axis) by age of TE (mya) (y-axis). TEs that mapped to hiPSCs (top), all repeats from human UCSC repeatmasker annotation (bottom). TEs are grouped by class and color-coded by family. (f) boxplots of age (mya) of TEs (y-axis) of young human L1s either detected or not detected in hiPSC dataset. detected: L1HS (n = 15), L1PA2 (n = 34), L1PA3 (n = 34), L1PA4 (n = 20), L1PA5 (n = 18), L1PA6 (n = 17), not detected: L1HS (n = 1692), L1PA2 (n = 5148), L1PA3 (n = 11194), L1PA4 (n = 12471), L1PA5 (n = 11735), L1PA6 (n = 6195). (g) boxplots of age (mya) of TEs (y-axis) of young mouse L1s either detected or not detected in mouse blastomeres. detected: L1MdA (n = 27), L1MdT (n = 44), L1MdF3 (n = 8), L1MdF2 (n = 43), L1MdGf (n = 1), L1MdF (n = 5), not detected: L1MdA (n = 16817), L1MdT (n = 23644), L1MdF3 (n = 16138), L1MdF2 (n = 64855), L1MdGf (n = 1079), L1MdF (n = 4011). The boxplots in A,F and G show the median, first and third quartiles as a box, and the whiskers indicate the most extreme data point within 1.5 lengths of the box.
