Fig. 3: Cell-type specific long read sequencing of a mobile ERV2 element.

a Schematic of PacBio SMRT circular consensus sequence (CCS) long-read sequencing workflow. De novo reads identified by evaluating BLAST bit scores between alignment to the IAPEzi consensus and the IAP-masked reference genome. b (Top) PacBio biotinylated oligonucleotide probe design. The probe sequences are the most divergent regions of IAPEzi across other repetitive elements with detectable homology (<10%, dfam.org). (Middle) Real time qPCR plot of genomic DNA vs. IAPEzi-captured DNA. (Bottom) Box and whisker plot documenting significant IAPEzi enrichment as compared to fossilized IAPEY3 repeat element (n = 6 biologically independent samples) (p = 0.008, Student’s t test, two-sided). c Subcompartment box-and-whiskers observed/expected plot (top) and mean observed/expected heatmap for IAPEzi de novo integration sites (bottom). Data shown for eight mouse cortical NeuN+ and NeuN− samples, and two round spermatid samples (totaling n = 10) from n = 7 biologically independent samples, as indicated. ‘Full’ de novo reads refer to de novo reads with >90% (5833/6481 bp) match with the IAPEzi consensus sequence length (dfam.org). Filled boxes refer to ‘all’ de novo, while outlined boxes refer to ‘full’ de novo. d Genome browser shot of chr4 with de novo IAPEzi insertions for each of 10 profiled adult cortex neuronal and non-neuronal samples and round spermatids, as indicated. Subcompartment designations as indicated. Arrows point to representative full-length de novo insertions in close genomic range of each other across different samples. Specific coordinates corresponding to all (green) vs. full (black) de novo in Data S12) Letters refer to de novo insertions labeled in Data S12 for reference. Source data, included mean ± SEM for the included boxplots, are provided as a Source Data file.