Additional file 1 of Chromatin modifier developmental pluripotency associated factor 4 (DPPA4) is a candidate gene for alcohol-induced developmental disorders

Additional file 1: Table S1. General information about PAE samples. Table S2. General information about control samples. Table S3. General characteristics of PAE, early PAE and control newborns as well as their mothers included in the genome-wide DNAm and mRNA-seq analyses. Table S4. Primers for EpiTYPER and ChIP-qPCR. Table S5. PCR protocols for EpiTYPER and ChIP-qPCR. Table S6. Antibodies for ChIP. Table S7. PAE-associated differentially methylated CpGs in the placenta analyzed by microarrays. Table S8. PAE-associated differentially methylated CpGs in the placenta: sensitivity analysis for DMPs. Table S9. PAE-associated differentially methylated CpGs in the placenta: sensitivity analysis for candidate genes. Table S10. PAE-associated DMRs in the placenta. Table S11. Early PAE-associated differentially methylated CpGs in the placenta. Table S12. Early PAE-associated differentially methylated CpGs in the placenta: sensitivity analysis for DMPs. Table S13. Early PAE-associated differentially methylated CpGs in the placenta: sensitivity analysis for candidate genes. Table S14. Early PAE-associated DMRs in the placenta. Table S15. PAE-associated differentially methylated CpGs in the placenta: adjusted by cell type. Table S16. PAE-associated DMRs in the placenta: adjusted by cell type. Table S17. Early PAE-associated differentially methylated CpGs in the placenta: adjusted by cell type. Table S18. Early PAE-associated DMRs in the placenta: adjusted by cell type. Table S19. Pathway analysis of placental DMPs. Table S20. Pathway analysis of placental DMRs. Table S21. Sample-specific normalized placental DNAm levels (analyzed by microarrays) of target genes selected for EpiTYPER analysis. Table S22. PAE-associated differentially expressed genes in the placenta analyzed by mRNA-seq. Table S23. Pathway analysis of differentially expressed genes in PAE placentas. Table S24. Early PAE-associated differentially expressed genes in the placenta. Table S25. Genes with significant PAE-associated correlation between placental DNAm and mRNA expression. Table S26. Alcohol-induced differentially methylated CpGs and mCpHs in hESCs analyzed by microarrays. Table S27. Alcohol-induced DMRs in hESCs. Table S28. Pathway analysis of DMPs in hESCs. Table S29. Pathway analysis of DMRs in hESCs. Table S30. Differentially expressed genes in alcohol-exposed hESCs analyzed by mRNA-seq. Table S31. Pathway analysis of differentially expressed genes in hESCs. Table S32. Genes with significant alcohol exposure-associated correlation between DNAm and mRNA expression in hESCs. Table S33. DNAm levels of DPPA4 regulatory region in alcohol-exposed and control hESCs analyzed by EpiTYPER. Table S34. Common alcohol exposure-associated genes in genome-wide DNAm and mRNA-seq analyses of placenta and hESCs. Table S35. Pathway analysis of common genes associated significantly with alcohol exposure in genome-wide DNAm analyses of placenta and hESCs. Table S36. Common genes in genome-wide DNAm analyses of placenta and hESCs previously associated with alcohol exposure. Table S37. Common genes and DMPs in genome-wide DNAm analysis of placenta previously associated with alcohol exposure in BECs of FASD or PAE children.