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Additional file 3. Review history.

Additional file 1. Supplementary Figures S1-S20.

Additional file 1: Fig. S1. The coinfection of HHVs in RE and TLE. (a) Coinfection by more than one HHVs in RE, TLE and TBI cases. (b)The cumulative viral scores, which were the cumulative scores of coinfected HHVs in a single case, were expressed as mean �� STD and analyzed with a two-tailed Student t test(**: p

Additional file 1. Additional Figures.

Figure S1, S2, S3 and Supplemental notes. Generation of AxinIAP and AIAP founder mice and copy number variation assays for AxincL1 mice (Figure S1); promoter activity analyses (Figure S2); DNA methylation levels around cL1 in penetrant and silent AxincL1 mice (Figure S3); and annotated sequences of retrotransposons used in this study (Supplemental notes). (PDF 5204 kb)

Additional file 1: Fig. S1. Principal component analysis (PCA) of control versus DDT genomic data sets for (A) DMRs and (B) DHRs in the F3 generation sperm. Separate clustering of the control and DDT data includes negligible overlap.

Additional file 3: Table S1. F1 DMR pÂ

Additional file 13: Fig. S5. Epimutation-associated gene pathways for endocytosis containing 5 DMRs (blue box), 5 ncRNA (red box) and 6 DHRs (pink box).

Additional file 5: Table S3. F3 DMR pÂ

Additional file 14: Fig. S6. Evaluation of the quality of the RNA-Seq data generated in this study. (A) Variations among biological replicates of the six RNA samples (pachytene RNP, pachytene polysome, round spermatid RNP, round spermatid polysome, elongating RNP and elongating polysome). The biological variation is reflected by the coefficient of variation to the power of two (CV2) of FPKM values for each gene. The CV2 represents a normalized measure of cross-replicate variability, which has been widely used for evaluating quality of RNA-Seq data. The data presented here show that the abundance of the genes varied between replicate RNA samples, especially for the ones with lower FPKM values, which is expected. (B) Scatterplot matrix showing the pairwise scatterplots of the log10-normalized FPKMÂ scores across biological replicates of all six RNA samples. (C) Density plots showing the distribution of log10-normalized FPKM scores across biological replicates of all six RNA samples. (D) Overdispersion plots demonstrating the estimated overdispersion for each sample as a quality control measure.

Additional file 11: Fig. S3. Genome Browser representative map of site with two DMRs, one ncRNA and one histone retention site on chromosome 22q. One exposed sequence tag (EST) is present.

Additional file 2: Fig. S2. DMR permutation analysis. (A) F1 generation control versus DDT lineage, (B) F2 generation control versus DDT lineage, (C) F3 generation control versus DDT lineage analysis. The number of DMRs for all comparisons in the permutation analyses. The vertical red line shows the number of DMRs found in the original full analysis. All DMRs are defined using an edgeR p value threshold of 1e−06. The number of DMRs in the control versus DDT lineage analysis is higher than would be expected due to random chance (p ≤ 0.1).

Additional file 8: Table S6. (A) F3 lncRNA p

Additional file 12: Fig. S4. Epimutation-associated gene pathway for the pathways in cancer containing 5 DMRs (blue box), 6 ncRNA (red box) and 7 DHRs (pink box).

Additional file 6: Table S4. (A) Site Table F1 lncRNA p

Additional file 10: Table S8. F3 H3K27me3 DHR pÂ

Additional file 7: Table S5. (A) F2 lncRNA p

Additional file 1: Fig. S1. Principal component analysis (PCA) of control versus DDT genomic data sets for (A) DMRs and (B) DHRs in the F3 generation sperm. Separate clustering of the control and DDT data includes negligible overlap.

Additional file 6: Table S4. (A) Site Table F1 lncRNA p

Additional file 2: Fig. S2. DMR permutation analysis. (A) F1 generation control versus DDT lineage, (B) F2 generation control versus DDT lineage, (C) F3 generation control versus DDT lineage analysis. The number of DMRs for all comparisons in the permutation analyses. The vertical red line shows the number of DMRs found in the original full analysis. All DMRs are defined using an edgeR p value threshold of 1e−06. The number of DMRs in the control versus DDT lineage analysis is higher than would be expected due to random chance (p ≤ 0.1).

Additional file 9: Table S7. F3 DHR pÂ

Additional file 8: Table S6. (A) F3 lncRNA p

Additional file 9: Table S7. F3 DHR pÂ

Additional file 12: Fig. S4. Epimutation-associated gene pathway for the pathways in cancer containing 5 DMRs (blue box), 6 ncRNA (red box) and 7 DHRs (pink box).

Additional file 10: Table S8. F3 H3K27me3 DHR pÂ

Additional file 7: Table S5. (A) F2 lncRNA p