Fig. 1

Setup of our study including reconstruction of PGA genotypes using allele-specific RNA-seq. a Mouse strains and crosses used to derive the B6D2F1 samples as profiled by RNA-seq. b Embryos were collected at different stages of development (top) and microdissected for RNA-seq as shown in the illustration (bottom) [28]. The epiblast is depicted in shades of pink, trophectoderm is in gray, extraembryonic endoderm is light brown, and extraembryonic mesoderm is dark brown. Dashed lines show the cells dissected for total RNA isolation. c Genotype of ESC lines as determined by allele-specific RNA-seq at 5 MB resolution. The horizontal axis represents chromosomes, and the vertical axis chromosomal bins (per 5 MB). The numbers within each bin (also categorized by the three colors) represent the percentage B6 as compared to the total coverage of B6 and DBA2. The panel of ESC1 shows the position of imprinted gene clusters that are included in follow-up analysis (Fig. 2). Additional file 2: Fig. S3 shows the genotype of all 8 B6D2F1 ESC lines profiled. d Distribution of relative expression of the B6 versus the DBA2 allele of the genes present within genomic regions genotyped as either homozygous B6 (red), heterozygous B6/DBA2 (blue) or homozygous DBA2 (yellow) in the ESC-PGAs. A log2 ratio of 0 represents equal biallelic gene expression from the B6 and DBA2 alleles, while positive and negative ratios represent higher expression from the B6 or DBA2 allele, respectively. e Similar to panel c, but showing EpiSC lines. Additional file 2: Fig. S5 shows the RNA-seq-based genotyping of all 8 DBA2 EpiSC lines profiled